Starting phenix.real_space_refine on Thu Aug 6 16:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pyk_72035/08_2026/9pyk_72035.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pyk_72035/08_2026/9pyk_72035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pyk_72035/08_2026/9pyk_72035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pyk_72035/08_2026/9pyk_72035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pyk_72035/08_2026/9pyk_72035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pyk_72035/08_2026/9pyk_72035.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 109 5.16 5 C 9878 2.51 5 N 2638 2.21 5 O 3148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15773 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 4335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4335 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 6 Chain: "B" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4288 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 23, 'TRANS': 519} Chain breaks: 7 Chain: "C" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4376 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 23, 'TRANS': 530} Chain breaks: 6 Chain: "H" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "D" 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: "G" 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" 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: "O" 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: "P" 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 3.78, per 1000 atoms: 0.24 Number of scatterers: 15773 At special positions: 0 Unit cell: (133.373, 127.17, 146.814, 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 109 16.00 O 3148 8.00 N 2638 7.00 C 9878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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=2.03 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=2.05 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=1.76 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 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.02 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN M 4 " - " MAN M 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 295 " " NAG A 703 " - " ASN A 301 " " NAG A 704 " - " ASN A 332 " " NAG A 705 " - " ASN A 133 " " NAG A 706 " - " ASN A 392 " " NAG A 707 " - " ASN A 448 " " NAG A 708 " - " ASN A 197 " " NAG A 709 " - " ASN A 234 " " NAG A 710 " - " ASN A 276 " " NAG A 711 " - " ASN A 363 " " NAG A 712 " - " ASN A 611 " " NAG B 701 " - " ASN B 197 " " NAG B 702 " - " ASN B 295 " " NAG B 703 " - " ASN B 301 " " NAG B 704 " - " ASN B 332 " " NAG B 705 " - " ASN B 133 " " NAG B 706 " - " ASN B 339 " " NAG B 707 " - " ASN B 448 " " NAG B 708 " - " ASN B 234 " " NAG B 709 " - " ASN B 276 " " NAG B 710 " - " ASN B 363 " " NAG C 701 " - " ASN C 197 " " NAG C 702 " - " ASN C 295 " " NAG C 703 " - " ASN C 301 " " NAG C 704 " - " ASN C 133 " " NAG C 705 " - " ASN C 339 " " NAG C 706 " - " ASN C 392 " " NAG C 707 " - " ASN C 448 " " NAG C 708 " - " ASN C 88 " " NAG C 709 " - " ASN C 234 " " NAG C 710 " - " ASN C 276 " " NAG C 711 " - " ASN C 386 " " NAG D 1 " - " ASN A 156 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN B 160 " " NAG I 1 " - " ASN B 156 " " NAG J 1 " - " ASN B 262 " " NAG K 1 " - " ASN B 386 " " NAG M 1 " - " ASN C 160 " " NAG N 1 " - " ASN C 332 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 262 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 739.6 milliseconds 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 27 sheets defined 25.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.244A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 removed outlier: 4.138A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.804A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.291A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.971A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 569 through 596 removed outlier: 4.229A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 635 through 649 removed outlier: 4.507A pdb=" N GLN A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.332A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 334 through 354 removed outlier: 3.513A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.156A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.815A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 484 removed outlier: 4.915A pdb=" N TYR B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 484' Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.814A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 546 removed outlier: 4.190A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.684A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 635 through 649 removed outlier: 4.570A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 661 removed outlier: 3.850A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.102A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.519A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.767A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.078A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.658A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.798A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 569 through 597 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.900A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.110A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.178A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.509A pdb=" N ILE A 251 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR A 217 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N HIS A 249 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.898A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.653A pdb=" N SER A 158 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 5.096A pdb=" N LYS A 305 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N MET A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 removed outlier: 4.490A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.622A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 495 through 497 Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.543A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 84 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 133 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 177 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100G through 103 Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.003A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 312 removed outlier: 7.184A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 323A current: chain 'B' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 381 through 385 current: chain 'B' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'C' and resid 495 through 497 Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.697A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 86 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.683A pdb=" N HIS C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 4.333A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS C 305 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N MET C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.122A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1248 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: 2.63 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4223 1.33 - 1.48: 4907 1.48 - 1.62: 6802 1.62 - 1.77: 3 1.77 - 1.91: 146 Bond restraints: 16081 Sorted by residual: bond pdb=" C ASN C 160 " pdb=" O ASN C 160 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.14e-02 7.69e+03 1.61e+01 bond pdb=" C ILE H 97 " pdb=" O ILE H 97 " ideal model delta sigma weight residual 1.237 1.195 0.043 1.13e-02 7.83e+03 1.42e+01 bond pdb=" N GLN C 653 " pdb=" CA GLN C 653 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.17e+01 bond pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " ideal model delta sigma weight residual 1.808 1.912 -0.104 3.30e-02 9.18e+02 9.89e+00 bond pdb=" C ARG H 98 " pdb=" O ARG H 98 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.25e-02 6.40e+03 9.64e+00 ... (remaining 16076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 21526 3.85 - 7.70: 282 7.70 - 11.55: 13 11.55 - 15.40: 1 15.40 - 19.25: 2 Bond angle restraints: 21824 Sorted by residual: angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 133.65 -19.25 2.30e+00 1.89e-01 7.00e+01 angle pdb=" CA CYS C 247 " pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 114.40 133.51 -19.11 2.30e+00 1.89e-01 6.90e+01 angle pdb=" N GLU C 648 " pdb=" CA GLU C 648 " pdb=" C GLU C 648 " ideal model delta sigma weight residual 113.41 105.07 8.34 1.22e+00 6.72e-01 4.67e+01 angle pdb=" C PRO B 81 " pdb=" CA PRO B 81 " pdb=" CB PRO B 81 " ideal model delta sigma weight residual 111.56 122.57 -11.01 1.65e+00 3.67e-01 4.45e+01 angle pdb=" N GLN B 82 " pdb=" CA GLN B 82 " pdb=" C GLN B 82 " ideal model delta sigma weight residual 112.04 103.56 8.48 1.44e+00 4.82e-01 3.47e+01 ... (remaining 21819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 9868 21.04 - 42.07: 497 42.07 - 63.11: 130 63.11 - 84.15: 48 84.15 - 105.19: 34 Dihedral angle restraints: 10577 sinusoidal: 5148 harmonic: 5429 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 167.37 -74.37 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 662 " pdb=" CB CYS B 662 " ideal model delta sinusoidal sigma weight residual 93.00 149.15 -56.15 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CD ARG C 166 " pdb=" NE ARG C 166 " pdb=" CZ ARG C 166 " pdb=" NH1 ARG C 166 " ideal model delta sinusoidal sigma weight residual 0.00 54.34 -54.34 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 10574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2463 0.117 - 0.233: 187 0.233 - 0.350: 8 0.350 - 0.467: 1 0.467 - 0.583: 2 Chirality restraints: 2661 Sorted by residual: chirality pdb=" C1 MAN G 5 " pdb=" O2 MAN G 4 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 1.82 0.58 2.00e-02 2.50e+03 8.51e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.15e+02 chirality pdb=" C1 MAN M 5 " pdb=" O2 MAN M 4 " pdb=" C2 MAN M 5 " pdb=" O5 MAN M 5 " both_signs ideal model delta sigma weight residual False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.20e+02 ... (remaining 2658 not shown) Planarity restraints: 2728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.256 2.00e-02 2.50e+03 2.19e-01 5.99e+02 pdb=" C7 NAG M 1 " 0.058 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.382 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 166 " 0.738 9.50e-02 1.11e+02 3.32e-01 7.58e+01 pdb=" NE ARG C 166 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 166 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG C 166 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 166 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 617 " -0.729 9.50e-02 1.11e+02 3.28e-01 7.38e+01 pdb=" NE ARG C 617 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG C 617 " -0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG C 617 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 617 " -0.005 2.00e-02 2.50e+03 ... (remaining 2725 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 1 2.31 - 2.96: 6988 2.96 - 3.60: 21214 3.60 - 4.25: 36274 4.25 - 4.90: 59287 Nonbonded interactions: 123764 Sorted by model distance: nonbonded pdb=" O LEU C 660 " pdb=" CD1 LEU C 661 " model vdw 1.659 3.460 nonbonded pdb=" O3 NAG M 1 " pdb=" O5 NAG M 2 " model vdw 2.373 3.040 nonbonded pdb=" N VAL C 182 " pdb=" O VAL C 182 " model vdw 2.506 2.496 nonbonded pdb=" ND2 ASN H 35 " pdb=" OD1 ASP H 95 " model vdw 2.513 3.120 nonbonded pdb=" N PRO B 81 " pdb=" O PRO B 81 " model vdw 2.521 2.496 ... (remaining 123759 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' and (resid 36 through 56 or resid 66 through 135 or resid 150 through \ 398 or resid 412 through 457 or resid 464 through 501 or resid 522 through 546 \ or resid 569 through 659 or resid 703 through 712)) selection = (chain 'B' and (resid 36 through 184 or resid 189 through 457 or resid 464 throu \ gh 501 or resid 522 through 659 or resid 701 through 710)) selection = (chain 'C' and (resid 36 through 56 or resid 66 through 135 or resid 150 through \ 184 or resid 189 through 398 or resid 412 through 457 or resid 464 through 501 \ or resid 522 through 546 or resid 569 through 659 or resid 702 through 711)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'P' } 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 individual isotropic 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: 5.290 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.007 0.273 16185 Z= 0.314 Angle : 1.172 24.379 22102 Z= 0.614 Chirality : 0.065 0.583 2661 Planarity : 0.016 0.332 2684 Dihedral : 15.258 105.186 6963 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.66 % Allowed : 10.82 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 1835 helix: 0.05 (0.26), residues: 387 sheet: 0.10 (0.22), residues: 511 loop : -0.17 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.003 ARG C 166 TYR 0.041 0.003 TYR C 486 PHE 0.028 0.003 PHE C 317 TRP 0.028 0.002 TRP C 479 HIS 0.009 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.29 (16081) covalent geometry : angle 1.11449 / 0.60 (21824) SS BOND : bond 0.04741 / 2.65 ( 34) SS BOND : angle 4.20677 / 3.15 ( 68) hydrogen bonds : bond 0.15459 / 10.88 ( 460) hydrogen bonds : angle 7.34745 / 5.20 ( 1248) link_ALPHA1-2 : bond 0.03716 / 1.90 ( 3) link_ALPHA1-2 : angle 5.84742 / 3.89 ( 9) link_ALPHA1-3 : bond 0.03344 / 1.64 ( 4) link_ALPHA1-3 : angle 4.21692 / 2.52 ( 12) link_ALPHA1-6 : bond 0.02032 / 1.07 ( 2) link_ALPHA1-6 : angle 4.47778 / 2.40 ( 6) link_BETA1-4 : bond 0.02084 / 1.36 ( 17) link_BETA1-4 : angle 3.56668 / 2.50 ( 51) link_NAG-ASN : bond 0.00418 / 0.31 ( 44) link_NAG-ASN : angle 2.37078 / 1.62 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 326 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7935 (mp0) cc_final: 0.7405 (tp30) REVERT: A 96 TRP cc_start: 0.6899 (m-90) cc_final: 0.6227 (m100) REVERT: A 207 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7542 (tmtt) REVERT: A 239 CYS cc_start: 0.6712 (t) cc_final: 0.6503 (t) REVERT: A 637 ASN cc_start: 0.7422 (m-40) cc_final: 0.7104 (t0) REVERT: A 652 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.5696 (tp40) REVERT: B 46 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8613 (mmmt) REVERT: B 53 PHE cc_start: 0.8565 (p90) cc_final: 0.8363 (p90) REVERT: B 360 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7651 (ttp80) REVERT: B 422 GLN cc_start: 0.8848 (mt0) cc_final: 0.8440 (mt0) REVERT: C 43 PRO cc_start: 0.8418 (Cg_endo) cc_final: 0.8171 (Cg_exo) REVERT: C 136 ASN cc_start: 0.7751 (m110) cc_final: 0.7190 (m-40) REVERT: C 138 ILE cc_start: 0.7903 (pt) cc_final: 0.7700 (pt) REVERT: C 191 TYR cc_start: 0.9064 (m-80) cc_final: 0.8583 (m-80) REVERT: C 650 GLN cc_start: 0.7543 (mp10) cc_final: 0.7139 (mt0) outliers start: 11 outliers final: 6 residues processed: 336 average time/residue: 0.1143 time to fit residues: 57.8096 Evaluate side-chains 227 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 56 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 HIS A 249 HIS A 352 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 348 GLN B 425 ASN B 478 ASN B 625 ASN C 72 HIS L 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.165467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140941 restraints weight = 20681.523| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.05 r_work: 0.3538 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16185 Z= 0.171 Angle : 0.686 13.390 22102 Z= 0.341 Chirality : 0.048 0.262 2661 Planarity : 0.004 0.046 2684 Dihedral : 9.744 78.388 3454 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.64 % Allowed : 13.04 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1835 helix: 0.83 (0.27), residues: 389 sheet: 0.39 (0.22), residues: 550 loop : -0.05 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 617 TYR 0.016 0.002 TYR H 100N PHE 0.020 0.002 PHE H 100M TRP 0.020 0.002 TRP B 479 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (16081) covalent geometry : angle 0.65320 / 0.33 (21824) SS BOND : bond 0.00468 / 0.31 ( 34) SS BOND : angle 1.27317 / 0.83 ( 68) hydrogen bonds : bond 0.04333 / 2.81 ( 460) hydrogen bonds : angle 5.59831 / 3.91 ( 1248) link_ALPHA1-2 : bond 0.00945 / 0.47 ( 3) link_ALPHA1-2 : angle 1.78246 / 1.12 ( 9) link_ALPHA1-3 : bond 0.01255 / 0.62 ( 4) link_ALPHA1-3 : angle 2.27325 / 1.75 ( 12) link_ALPHA1-6 : bond 0.00684 / 0.34 ( 2) link_ALPHA1-6 : angle 1.74276 / 1.01 ( 6) link_BETA1-4 : bond 0.00542 / 0.31 ( 17) link_BETA1-4 : angle 2.13225 / 1.52 ( 51) link_NAG-ASN : bond 0.00315 / 0.21 ( 44) link_NAG-ASN : angle 2.20535 / 1.49 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7872 (mp0) cc_final: 0.7277 (tp30) REVERT: A 276 ASN cc_start: 0.4888 (OUTLIER) cc_final: 0.4617 (m110) REVERT: A 637 ASN cc_start: 0.7629 (m-40) cc_final: 0.7252 (t0) REVERT: A 652 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6278 (mm110) REVERT: B 360 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7553 (ttt90) REVERT: B 422 GLN cc_start: 0.8882 (mt0) cc_final: 0.8631 (mt0) REVERT: C 43 PRO cc_start: 0.8416 (Cg_endo) cc_final: 0.8038 (Cg_exo) REVERT: C 91 GLU cc_start: 0.7668 (tp30) cc_final: 0.7449 (tp30) REVERT: C 136 ASN cc_start: 0.7739 (m110) cc_final: 0.7153 (m-40) REVERT: C 138 ILE cc_start: 0.8022 (pt) cc_final: 0.7696 (pt) REVERT: C 370 GLU cc_start: 0.7395 (mp0) cc_final: 0.7079 (mp0) REVERT: C 530 MET cc_start: 0.7331 (mmm) cc_final: 0.6828 (mtt) REVERT: C 633 LYS cc_start: 0.7830 (mptt) cc_final: 0.7573 (mptt) REVERT: C 657 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.5580 (pp20) outliers start: 44 outliers final: 24 residues processed: 265 average time/residue: 0.1141 time to fit residues: 45.7804 Evaluate side-chains 223 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 56 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN H 100KASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137629 restraints weight = 20993.994| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.06 r_work: 0.3469 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16185 Z= 0.209 Angle : 0.681 12.571 22102 Z= 0.337 Chirality : 0.048 0.228 2661 Planarity : 0.004 0.049 2684 Dihedral : 8.204 69.323 3448 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 3.91 % Allowed : 12.50 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1835 helix: 0.86 (0.27), residues: 390 sheet: 0.27 (0.21), residues: 567 loop : -0.17 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 64 TYR 0.016 0.002 TYR H 100N PHE 0.017 0.002 PHE L 98 TRP 0.022 0.002 TRP A 96 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (16081) covalent geometry : angle 0.65064 / 0.33 (21824) SS BOND : bond 0.00541 / 0.34 ( 34) SS BOND : angle 1.26288 / 0.86 ( 68) hydrogen bonds : bond 0.04246 / 2.80 ( 460) hydrogen bonds : angle 5.32864 / 3.71 ( 1248) link_ALPHA1-2 : bond 0.00731 / 0.37 ( 3) link_ALPHA1-2 : angle 1.82975 / 1.15 ( 9) link_ALPHA1-3 : bond 0.01073 / 0.54 ( 4) link_ALPHA1-3 : angle 1.75555 / 1.29 ( 12) link_ALPHA1-6 : bond 0.00720 / 0.35 ( 2) link_ALPHA1-6 : angle 1.79204 / 1.07 ( 6) link_BETA1-4 : bond 0.00409 / 0.25 ( 17) link_BETA1-4 : angle 2.05123 / 1.47 ( 51) link_NAG-ASN : bond 0.00337 / 0.25 ( 44) link_NAG-ASN : angle 2.13518 / 1.44 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7958 (mp0) cc_final: 0.7352 (tp30) REVERT: A 138 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6846 (pp) REVERT: A 454 LEU cc_start: 0.8510 (mp) cc_final: 0.8204 (mp) REVERT: A 637 ASN cc_start: 0.7802 (m-40) cc_final: 0.7148 (t0) REVERT: A 650 GLN cc_start: 0.7719 (tp40) cc_final: 0.7418 (tp40) REVERT: A 652 GLN cc_start: 0.6606 (OUTLIER) cc_final: 0.6229 (mm110) REVERT: B 199 SER cc_start: 0.8946 (m) cc_final: 0.8732 (m) REVERT: B 360 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7542 (ttt90) REVERT: C 43 PRO cc_start: 0.8538 (Cg_endo) cc_final: 0.8133 (Cg_exo) REVERT: C 91 GLU cc_start: 0.7648 (tp30) cc_final: 0.7436 (tp30) REVERT: C 138 ILE cc_start: 0.8112 (pt) cc_final: 0.7807 (pt) REVERT: C 622 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6805 (mt) outliers start: 65 outliers final: 43 residues processed: 256 average time/residue: 0.0988 time to fit residues: 39.3829 Evaluate side-chains 224 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN ** H 35 ASN ** 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 = 0.3866 r_free = 0.3866 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132079 restraints weight = 20957.972| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.26 r_work: 0.3410 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16185 Z= 0.228 Angle : 0.706 19.626 22102 Z= 0.344 Chirality : 0.052 0.834 2661 Planarity : 0.004 0.045 2684 Dihedral : 7.696 64.280 3444 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 4.15 % Allowed : 13.58 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1835 helix: 0.83 (0.27), residues: 390 sheet: 0.07 (0.21), residues: 576 loop : -0.23 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.021 0.002 TYR H 100N PHE 0.016 0.002 PHE C 159 TRP 0.040 0.002 TRP A 96 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (16081) covalent geometry : angle 0.65368 / 0.33 (21824) SS BOND : bond 0.00584 / 0.41 ( 34) SS BOND : angle 1.39263 / 0.94 ( 68) hydrogen bonds : bond 0.04108 / 2.70 ( 460) hydrogen bonds : angle 5.23827 / 3.67 ( 1248) link_ALPHA1-2 : bond 0.00827 / 0.41 ( 3) link_ALPHA1-2 : angle 1.99561 / 1.28 ( 9) link_ALPHA1-3 : bond 0.01201 / 0.60 ( 4) link_ALPHA1-3 : angle 1.96253 / 1.50 ( 12) link_ALPHA1-6 : bond 0.00817 / 0.40 ( 2) link_ALPHA1-6 : angle 1.86056 / 1.12 ( 6) link_BETA1-4 : bond 0.00391 / 0.24 ( 17) link_BETA1-4 : angle 1.92011 / 1.37 ( 51) link_NAG-ASN : bond 0.00442 / 0.29 ( 44) link_NAG-ASN : angle 3.09828 / 2.16 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8002 (mp0) cc_final: 0.7268 (tp30) REVERT: A 138 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6675 (pp) REVERT: A 207 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7402 (tmtt) REVERT: A 454 LEU cc_start: 0.8628 (mp) cc_final: 0.8415 (mp) REVERT: A 637 ASN cc_start: 0.7746 (m-40) cc_final: 0.7023 (t0) REVERT: A 652 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6276 (mm110) REVERT: B 51 THR cc_start: 0.9256 (m) cc_final: 0.8799 (p) REVERT: B 199 SER cc_start: 0.9005 (m) cc_final: 0.8606 (m) REVERT: B 360 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7487 (ttt90) REVERT: C 138 ILE cc_start: 0.8175 (pt) cc_final: 0.7857 (pt) REVERT: C 657 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6044 (pp20) outliers start: 69 outliers final: 49 residues processed: 243 average time/residue: 0.1056 time to fit residues: 39.9694 Evaluate side-chains 222 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 168 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 184 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 656 ASN C 195 ASN ** H 35 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.159290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134006 restraints weight = 20775.089| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.26 r_work: 0.3466 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16185 Z= 0.146 Angle : 0.634 17.433 22102 Z= 0.310 Chirality : 0.049 0.685 2661 Planarity : 0.004 0.044 2684 Dihedral : 7.272 60.571 3444 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 3.49 % Allowed : 14.72 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1835 helix: 0.97 (0.27), residues: 390 sheet: 0.11 (0.22), residues: 579 loop : -0.29 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 350 TYR 0.015 0.001 TYR H 100N PHE 0.012 0.001 PHE A 233 TRP 0.066 0.002 TRP A 96 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16081) covalent geometry : angle 0.58328 / 0.30 (21824) SS BOND : bond 0.00461 / 0.33 ( 34) SS BOND : angle 1.21737 / 0.83 ( 68) hydrogen bonds : bond 0.03798 / 2.50 ( 460) hydrogen bonds : angle 5.06316 / 3.56 ( 1248) link_ALPHA1-2 : bond 0.00795 / 0.40 ( 3) link_ALPHA1-2 : angle 1.84102 / 1.15 ( 9) link_ALPHA1-3 : bond 0.01131 / 0.56 ( 4) link_ALPHA1-3 : angle 1.73476 / 1.36 ( 12) link_ALPHA1-6 : bond 0.00877 / 0.43 ( 2) link_ALPHA1-6 : angle 1.83559 / 1.13 ( 6) link_BETA1-4 : bond 0.00396 / 0.22 ( 17) link_BETA1-4 : angle 1.72806 / 1.25 ( 51) link_NAG-ASN : bond 0.00444 / 0.26 ( 44) link_NAG-ASN : angle 2.90985 / 2.01 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7959 (mp0) cc_final: 0.7250 (tp30) REVERT: A 138 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6672 (pp) REVERT: A 479 TRP cc_start: 0.7806 (m-10) cc_final: 0.7256 (m-10) REVERT: A 637 ASN cc_start: 0.7469 (m-40) cc_final: 0.6805 (t0) REVERT: A 652 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6172 (mm110) REVERT: B 199 SER cc_start: 0.8901 (m) cc_final: 0.8487 (m) REVERT: B 322 ASP cc_start: 0.8088 (p0) cc_final: 0.7820 (p0) REVERT: B 360 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7426 (ttt90) REVERT: C 138 ILE cc_start: 0.8173 (pt) cc_final: 0.7867 (pt) REVERT: C 189 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7800 (tttp) REVERT: C 657 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6018 (pp20) outliers start: 58 outliers final: 44 residues processed: 241 average time/residue: 0.1036 time to fit residues: 38.7190 Evaluate side-chains 229 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN B 656 ASN ** H 35 ASN ** 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 = 0.3873 r_free = 0.3873 target = 0.158061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132588 restraints weight = 20840.606| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.25 r_work: 0.3441 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16185 Z= 0.169 Angle : 0.636 15.761 22102 Z= 0.313 Chirality : 0.049 0.666 2661 Planarity : 0.004 0.044 2684 Dihedral : 6.929 58.308 3444 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer: Outliers : 3.85 % Allowed : 14.54 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1835 helix: 0.95 (0.27), residues: 392 sheet: 0.03 (0.22), residues: 571 loop : -0.31 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 617 TYR 0.013 0.001 TYR H 100N PHE 0.012 0.002 PHE L 98 TRP 0.077 0.002 TRP A 96 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (16081) covalent geometry : angle 0.58928 / 0.30 (21824) SS BOND : bond 0.00468 / 0.33 ( 34) SS BOND : angle 1.21190 / 0.82 ( 68) hydrogen bonds : bond 0.03781 / 2.50 ( 460) hydrogen bonds : angle 5.01827 / 3.53 ( 1248) link_ALPHA1-2 : bond 0.00771 / 0.39 ( 3) link_ALPHA1-2 : angle 1.86705 / 1.16 ( 9) link_ALPHA1-3 : bond 0.01078 / 0.54 ( 4) link_ALPHA1-3 : angle 1.68493 / 1.33 ( 12) link_ALPHA1-6 : bond 0.00889 / 0.43 ( 2) link_ALPHA1-6 : angle 1.77038 / 1.11 ( 6) link_BETA1-4 : bond 0.00391 / 0.23 ( 17) link_BETA1-4 : angle 1.71307 / 1.23 ( 51) link_NAG-ASN : bond 0.00349 / 0.25 ( 44) link_NAG-ASN : angle 2.79210 / 1.91 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7997 (mp0) cc_final: 0.7198 (tp30) REVERT: A 138 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6711 (pp) REVERT: A 207 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7311 (tmtt) REVERT: A 318 TYR cc_start: 0.8203 (m-80) cc_final: 0.7997 (m-80) REVERT: A 479 TRP cc_start: 0.7784 (m-10) cc_final: 0.7283 (m-10) REVERT: A 637 ASN cc_start: 0.7572 (m-40) cc_final: 0.6810 (t0) REVERT: A 652 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.6148 (mm110) REVERT: B 199 SER cc_start: 0.8996 (m) cc_final: 0.8585 (m) REVERT: B 322 ASP cc_start: 0.8100 (p0) cc_final: 0.7426 (p0) REVERT: B 360 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7408 (ttt90) REVERT: C 138 ILE cc_start: 0.8219 (pt) cc_final: 0.7921 (pt) REVERT: C 189 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7886 (tttp) REVERT: C 657 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5933 (pp20) outliers start: 64 outliers final: 49 residues processed: 249 average time/residue: 0.0992 time to fit residues: 38.2285 Evaluate side-chains 238 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 115 optimal weight: 0.0070 chunk 184 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** 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 = 0.3889 r_free = 0.3889 target = 0.159447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133664 restraints weight = 20786.127| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.33 r_work: 0.3430 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16185 Z= 0.144 Angle : 0.623 14.164 22102 Z= 0.304 Chirality : 0.048 0.644 2661 Planarity : 0.004 0.053 2684 Dihedral : 6.697 59.008 3444 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 3.61 % Allowed : 15.14 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1835 helix: 1.02 (0.27), residues: 392 sheet: -0.04 (0.21), residues: 581 loop : -0.25 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 617 TYR 0.012 0.001 TYR A 40 PHE 0.012 0.001 PHE A 233 TRP 0.053 0.001 TRP A 96 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (16081) covalent geometry : angle 0.58031 / 0.29 (21824) SS BOND : bond 0.00427 / 0.30 ( 34) SS BOND : angle 1.12370 / 0.76 ( 68) hydrogen bonds : bond 0.03631 / 2.39 ( 460) hydrogen bonds : angle 4.95174 / 3.47 ( 1248) link_ALPHA1-2 : bond 0.00776 / 0.39 ( 3) link_ALPHA1-2 : angle 1.80216 / 1.11 ( 9) link_ALPHA1-3 : bond 0.01044 / 0.52 ( 4) link_ALPHA1-3 : angle 1.61110 / 1.29 ( 12) link_ALPHA1-6 : bond 0.00873 / 0.42 ( 2) link_ALPHA1-6 : angle 1.72846 / 1.10 ( 6) link_BETA1-4 : bond 0.00405 / 0.23 ( 17) link_BETA1-4 : angle 1.62236 / 1.18 ( 51) link_NAG-ASN : bond 0.00486 / 0.26 ( 44) link_NAG-ASN : angle 2.67142 / 1.83 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8021 (mp0) cc_final: 0.7238 (tp30) REVERT: A 96 TRP cc_start: 0.7268 (m-10) cc_final: 0.6484 (m-10) REVERT: A 207 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7244 (tmtt) REVERT: A 479 TRP cc_start: 0.7763 (m-10) cc_final: 0.7331 (m-10) REVERT: A 637 ASN cc_start: 0.7584 (m-40) cc_final: 0.6815 (t0) REVERT: A 652 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.6061 (mm110) REVERT: B 199 SER cc_start: 0.8964 (m) cc_final: 0.8754 (m) REVERT: B 246 GLN cc_start: 0.7726 (tp40) cc_final: 0.7504 (tp40) REVERT: B 360 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7437 (ttt90) REVERT: C 43 PRO cc_start: 0.8396 (Cg_endo) cc_final: 0.8028 (Cg_exo) REVERT: C 138 ILE cc_start: 0.8228 (pt) cc_final: 0.7927 (pt) REVERT: C 189 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7900 (tttp) REVERT: C 657 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5997 (pp20) REVERT: C 660 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5313 (mt) outliers start: 60 outliers final: 47 residues processed: 248 average time/residue: 0.1045 time to fit residues: 40.3303 Evaluate side-chains 234 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 48 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 146 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 590 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 625 ASN ** H 35 ASN ** 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 = 0.3900 r_free = 0.3900 target = 0.160270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134689 restraints weight = 20909.337| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.31 r_work: 0.3475 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16185 Z= 0.131 Angle : 0.616 13.583 22102 Z= 0.299 Chirality : 0.047 0.648 2661 Planarity : 0.004 0.050 2684 Dihedral : 6.456 59.671 3444 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.79 % Allowed : 15.50 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1835 helix: 1.12 (0.28), residues: 394 sheet: -0.03 (0.21), residues: 576 loop : -0.25 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 617 TYR 0.010 0.001 TYR H 31 PHE 0.011 0.001 PHE A 233 TRP 0.042 0.001 TRP A 96 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (16081) covalent geometry : angle 0.57449 / 0.29 (21824) SS BOND : bond 0.00401 / 0.28 ( 34) SS BOND : angle 1.09655 / 0.75 ( 68) hydrogen bonds : bond 0.03521 / 2.32 ( 460) hydrogen bonds : angle 4.86081 / 3.40 ( 1248) link_ALPHA1-2 : bond 0.00828 / 0.42 ( 3) link_ALPHA1-2 : angle 1.75391 / 1.08 ( 9) link_ALPHA1-3 : bond 0.00985 / 0.49 ( 4) link_ALPHA1-3 : angle 1.54712 / 1.24 ( 12) link_ALPHA1-6 : bond 0.00844 / 0.41 ( 2) link_ALPHA1-6 : angle 1.73488 / 1.11 ( 6) link_BETA1-4 : bond 0.00419 / 0.24 ( 17) link_BETA1-4 : angle 1.61779 / 1.17 ( 51) link_NAG-ASN : bond 0.00511 / 0.28 ( 44) link_NAG-ASN : angle 2.60074 / 1.77 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7953 (mp0) cc_final: 0.7214 (tp30) REVERT: A 96 TRP cc_start: 0.7175 (m-10) cc_final: 0.6505 (m-10) REVERT: A 138 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6746 (pp) REVERT: A 479 TRP cc_start: 0.7682 (m-10) cc_final: 0.7294 (m-10) REVERT: A 637 ASN cc_start: 0.7446 (m-40) cc_final: 0.6693 (t0) REVERT: B 51 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.8992 (p) REVERT: B 150 MET cc_start: 0.5012 (tpt) cc_final: 0.4477 (tpp) REVERT: B 153 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: B 199 SER cc_start: 0.8947 (m) cc_final: 0.8726 (m) REVERT: B 322 ASP cc_start: 0.8031 (p0) cc_final: 0.7661 (p0) REVERT: B 360 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7397 (ttt90) REVERT: C 138 ILE cc_start: 0.8201 (pt) cc_final: 0.7894 (pt) REVERT: C 189 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7915 (tttp) REVERT: C 535 MET cc_start: 0.7286 (tpp) cc_final: 0.6876 (tpp) REVERT: C 657 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5920 (pp20) REVERT: L 74 THR cc_start: 0.8848 (m) cc_final: 0.8622 (m) outliers start: 63 outliers final: 50 residues processed: 241 average time/residue: 0.1045 time to fit residues: 38.7684 Evaluate side-chains 233 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 136 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN B 656 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.159292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136235 restraints weight = 20844.102| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.09 r_work: 0.3453 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16185 Z= 0.169 Angle : 0.641 13.221 22102 Z= 0.311 Chirality : 0.048 0.628 2661 Planarity : 0.004 0.054 2684 Dihedral : 6.329 59.025 3441 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 3.91 % Allowed : 15.62 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1835 helix: 1.13 (0.28), residues: 394 sheet: -0.00 (0.21), residues: 576 loop : -0.29 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 617 TYR 0.011 0.001 TYR B 638 PHE 0.012 0.001 PHE B 317 TRP 0.042 0.002 TRP A 631 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (16081) covalent geometry : angle 0.60052 / 0.30 (21824) SS BOND : bond 0.00437 / 0.31 ( 34) SS BOND : angle 1.21204 / 0.82 ( 68) hydrogen bonds : bond 0.03673 / 2.42 ( 460) hydrogen bonds : angle 4.91790 / 3.43 ( 1248) link_ALPHA1-2 : bond 0.00791 / 0.40 ( 3) link_ALPHA1-2 : angle 1.80640 / 1.13 ( 9) link_ALPHA1-3 : bond 0.00946 / 0.47 ( 4) link_ALPHA1-3 : angle 1.60305 / 1.26 ( 12) link_ALPHA1-6 : bond 0.00817 / 0.39 ( 2) link_ALPHA1-6 : angle 1.80842 / 1.14 ( 6) link_BETA1-4 : bond 0.00397 / 0.23 ( 17) link_BETA1-4 : angle 1.69871 / 1.21 ( 51) link_NAG-ASN : bond 0.00479 / 0.27 ( 44) link_NAG-ASN : angle 2.59505 / 1.77 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6789 (pp) REVERT: A 207 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7307 (tmtt) REVERT: A 479 TRP cc_start: 0.7690 (m-10) cc_final: 0.7313 (m-10) REVERT: A 637 ASN cc_start: 0.7497 (m-40) cc_final: 0.6721 (t0) REVERT: B 51 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.8988 (p) REVERT: B 150 MET cc_start: 0.5205 (tpt) cc_final: 0.4663 (tpp) REVERT: B 153 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: B 199 SER cc_start: 0.8962 (m) cc_final: 0.8585 (m) REVERT: B 360 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7474 (ttt90) REVERT: C 43 PRO cc_start: 0.8394 (Cg_endo) cc_final: 0.8022 (Cg_exo) REVERT: C 138 ILE cc_start: 0.8319 (pt) cc_final: 0.8045 (pt) REVERT: C 189 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7875 (tttp) REVERT: C 535 MET cc_start: 0.7223 (tpp) cc_final: 0.6855 (tpp) REVERT: C 657 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5981 (pp20) REVERT: H 38 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8073 (ptp90) outliers start: 65 outliers final: 51 residues processed: 232 average time/residue: 0.1222 time to fit residues: 43.5282 Evaluate side-chains 235 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 87 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 161 optimal weight: 0.0470 chunk 2 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 156 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** H 35 ASN ** 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 = 0.3908 r_free = 0.3908 target = 0.160813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136023 restraints weight = 20757.469| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.25 r_work: 0.3469 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16185 Z= 0.129 Angle : 0.614 13.703 22102 Z= 0.298 Chirality : 0.047 0.607 2661 Planarity : 0.004 0.052 2684 Dihedral : 6.161 59.029 3441 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.25 % Allowed : 16.41 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1835 helix: 1.18 (0.28), residues: 394 sheet: -0.03 (0.21), residues: 577 loop : -0.29 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 542 TYR 0.010 0.001 TYR C 486 PHE 0.011 0.001 PHE A 233 TRP 0.050 0.002 TRP A 631 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (16081) covalent geometry : angle 0.57446 / 0.29 (21824) SS BOND : bond 0.00398 / 0.28 ( 34) SS BOND : angle 1.10005 / 0.75 ( 68) hydrogen bonds : bond 0.03503 / 2.32 ( 460) hydrogen bonds : angle 4.84956 / 3.38 ( 1248) link_ALPHA1-2 : bond 0.00847 / 0.43 ( 3) link_ALPHA1-2 : angle 1.73384 / 1.07 ( 9) link_ALPHA1-3 : bond 0.00915 / 0.46 ( 4) link_ALPHA1-3 : angle 1.54013 / 1.22 ( 12) link_ALPHA1-6 : bond 0.00805 / 0.38 ( 2) link_ALPHA1-6 : angle 1.79092 / 1.14 ( 6) link_BETA1-4 : bond 0.00418 / 0.24 ( 17) link_BETA1-4 : angle 1.60667 / 1.16 ( 51) link_NAG-ASN : bond 0.00478 / 0.26 ( 44) link_NAG-ASN : angle 2.51733 / 1.72 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8136 (mp0) cc_final: 0.7384 (tp30) REVERT: A 138 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6733 (pp) REVERT: A 479 TRP cc_start: 0.7727 (m-10) cc_final: 0.7342 (m-10) REVERT: A 637 ASN cc_start: 0.7392 (m-40) cc_final: 0.6621 (t0) REVERT: B 51 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9072 (p) REVERT: B 150 MET cc_start: 0.4987 (tpt) cc_final: 0.4477 (tpp) REVERT: B 153 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: B 199 SER cc_start: 0.8977 (m) cc_final: 0.8760 (m) REVERT: B 360 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7399 (ttt90) REVERT: C 138 ILE cc_start: 0.8255 (pt) cc_final: 0.8028 (pt) REVERT: C 189 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7903 (tttp) REVERT: C 657 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5862 (pp20) REVERT: L 74 THR cc_start: 0.8832 (m) cc_final: 0.8625 (m) outliers start: 54 outliers final: 47 residues processed: 226 average time/residue: 0.1184 time to fit residues: 41.7218 Evaluate side-chains 230 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 166 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN B 590 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** H 35 ASN ** 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 = 0.3882 r_free = 0.3882 target = 0.158584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135358 restraints weight = 20885.112| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.04 r_work: 0.3444 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16185 Z= 0.175 Angle : 0.639 13.909 22102 Z= 0.311 Chirality : 0.048 0.573 2661 Planarity : 0.004 0.053 2684 Dihedral : 6.236 59.451 3441 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.73 % Allowed : 15.99 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1835 helix: 1.13 (0.27), residues: 393 sheet: -0.06 (0.22), residues: 574 loop : -0.29 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 542 TYR 0.011 0.002 TYR C 643 PHE 0.012 0.002 PHE B 53 TRP 0.046 0.002 TRP A 631 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (16081) covalent geometry : angle 0.59920 / 0.30 (21824) SS BOND : bond 0.00454 / 0.32 ( 34) SS BOND : angle 1.22766 / 0.83 ( 68) hydrogen bonds : bond 0.03706 / 2.43 ( 460) hydrogen bonds : angle 4.95720 / 3.45 ( 1248) link_ALPHA1-2 : bond 0.00772 / 0.39 ( 3) link_ALPHA1-2 : angle 1.83411 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00886 / 0.44 ( 4) link_ALPHA1-3 : angle 1.61915 / 1.26 ( 12) link_ALPHA1-6 : bond 0.00822 / 0.39 ( 2) link_ALPHA1-6 : angle 1.81733 / 1.14 ( 6) link_BETA1-4 : bond 0.00385 / 0.23 ( 17) link_BETA1-4 : angle 1.70713 / 1.22 ( 51) link_NAG-ASN : bond 0.00467 / 0.27 ( 44) link_NAG-ASN : angle 2.53921 / 1.73 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3896.34 seconds wall clock time: 67 minutes 28.86 seconds (4048.86 seconds total)