Starting phenix.real_space_refine on Thu Sep 18 09:13:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhj_49413/09_2025/9nhj_49413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhj_49413/09_2025/9nhj_49413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nhj_49413/09_2025/9nhj_49413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhj_49413/09_2025/9nhj_49413.map" model { file = "/net/cci-nas-00/data/ceres_data/9nhj_49413/09_2025/9nhj_49413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhj_49413/09_2025/9nhj_49413.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.042 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 107 5.16 5 C 9631 2.51 5 N 2595 2.21 5 O 3104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15437 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 640 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'TRANS': 123} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 120 Planarities with less than four sites: {'UNK:plan-1': 120} Unresolved non-hydrogen planarities: 120 Chain: "L" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 542 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'UNK:plan-1': 101} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3380 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 3 Chain: "G" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 955 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3393 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 3 Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3424 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "E" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1114 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 1 Chain: "F" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 955 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "B" 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: "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: 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: "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: 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: "Q" 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: "R" 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: "S" 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "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 Time building chain proxies: 3.90, per 1000 atoms: 0.25 Number of scatterers: 15437 At special positions: 0 Unit cell: (143.165, 133.76, 119.13, 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 107 16.00 O 3104 8.00 N 2595 7.00 C 9631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS E 664 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 664 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 664 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA P 3 " - " MAN P 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 413 " " NAG A 604 " - " ASN A 448 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 130 " " NAG A 607 " - " ASN A 197 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 241 " " NAG B 1 " - " ASN A 156 " " NAG C 601 " - " ASN C 301 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 130 " " NAG C 605 " - " ASN C 197 " " NAG C 606 " - " ASN C 230 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 386 " " NAG C 610 " - " ASN C 392 " " NAG C 611 " - " ASN C 398 " " NAG C 612 " - " ASN C 276 " " NAG C 613 " - " ASN C 234 " " NAG D 601 " - " ASN D 197 " " NAG D 602 " - " ASN D 160 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 234 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 289 " " NAG D 607 " - " ASN D 448 " " NAG D 608 " - " ASN D 295 " " NAG D 609 " - " ASN D 413 " " NAG D 610 " - " ASN D 332 " " NAG D 611 " - " ASN D 301 " " NAG D 612 " - " ASN D 386 " " NAG D 613 " - " ASN D 392 " " NAG D 614 " - " ASN D 398 " " NAG D 615 " - " ASN D 88 " " NAG E 701 " - " ASN E 656 " " NAG E 702 " - " ASN E 611 " " NAG E 703 " - " ASN E 625 " " NAG E 704 " - " ASN E 616 " " NAG E 705 " - " ASN E 637 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 656 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN C 88 " " NAG K 1 " - " ASN C 156 " " NAG M 1 " - " ASN C 332 " " NAG N 1 " - " ASN C 413 " " NAG O 1 " - " ASN C 448 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN D 241 " " NAG R 1 " - " ASN D 156 " " NAG S 1 " - " ASN D 262 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 610.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 27 sheets defined 26.9% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'H' and resid 62 through 68 removed outlier: 5.080A pdb=" N UNK H 66 " --> pdb=" O UNK H 63 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N UNK H 68 " --> pdb=" O UNK H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.872A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.953A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.745A pdb=" N GLN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 572 through 596 Processing helix chain 'G' and resid 618 through 624 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 641 through 657 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.847A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.642A pdb=" N MET C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.711A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.849A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 334 through 350 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 476 through 484 removed outlier: 3.959A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 521 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 546 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 573 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 660 removed outlier: 3.508A pdb=" N THR E 658 " --> pdb=" O GLU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 664 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.306A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 removed outlier: 3.672A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 4.029A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 659 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 8 removed outlier: 4.548A pdb=" N UNK H 16 " --> pdb=" O UNK H 85 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N UNK H 85 " --> pdb=" O UNK H 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 32 through 39 removed outlier: 6.139A pdb=" N UNK H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 60 current: chain 'H' and resid 113 through 116 Processing sheet with id=AA3, first strand: chain 'H' and resid 108 through 109 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.311A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AB3, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.566A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG A 315 " --> 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 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 382 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.446A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.040A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB9, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.887A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, 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: 6.830A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG C 315 " --> 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 465 through 470 Processing sheet with id=AC2, first strand: chain 'D' and resid 494 through 497 Processing sheet with id=AC3, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.713A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.966A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 312 removed outlier: 6.970A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 315 through 323A current: chain 'D' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 393 through 395 current: chain 'D' and resid 465 through 470 Processing sheet with id=AC9, first strand: chain 'D' and resid 374 through 378 481 hydrogen bonds defined for protein. 1335 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: 2.71 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4239 1.33 - 1.46: 4346 1.46 - 1.59: 6986 1.59 - 1.72: 1 1.72 - 1.85: 140 Bond restraints: 15712 Sorted by residual: bond pdb=" CG1 ILE A 449 " pdb=" CD1 ILE A 449 " ideal model delta sigma weight residual 1.513 1.596 -0.083 3.90e-02 6.57e+02 4.54e+00 bond pdb=" CB ILE A 449 " pdb=" CG2 ILE A 449 " ideal model delta sigma weight residual 1.521 1.578 -0.057 3.30e-02 9.18e+02 2.93e+00 bond pdb=" CB ILE D 181 " pdb=" CG2 ILE D 181 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" N UNK H 1 " pdb=" CA UNK H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CB ILE D 184 " pdb=" CG2 ILE D 184 " ideal model delta sigma weight residual 1.521 1.573 -0.052 3.30e-02 9.18e+02 2.45e+00 ... (remaining 15707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 19300 1.60 - 3.20: 1781 3.20 - 4.80: 241 4.80 - 6.40: 53 6.40 - 8.00: 7 Bond angle restraints: 21382 Sorted by residual: angle pdb=" N ILE G 595 " pdb=" CA ILE G 595 " pdb=" C ILE G 595 " ideal model delta sigma weight residual 111.44 105.53 5.91 1.34e+00 5.57e-01 1.94e+01 angle pdb=" N TRP G 596 " pdb=" CA TRP G 596 " pdb=" C TRP G 596 " ideal model delta sigma weight residual 110.55 104.88 5.67 1.35e+00 5.49e-01 1.76e+01 angle pdb=" N TRP E 596 " pdb=" CA TRP E 596 " pdb=" C TRP E 596 " ideal model delta sigma weight residual 110.55 105.30 5.25 1.35e+00 5.49e-01 1.51e+01 angle pdb=" C UNK L 105 " pdb=" N UNK L 106 " pdb=" CA UNK L 106 " ideal model delta sigma weight residual 121.70 128.41 -6.71 1.80e+00 3.09e-01 1.39e+01 angle pdb=" N VAL G 539 " pdb=" CA VAL G 539 " pdb=" C VAL G 539 " ideal model delta sigma weight residual 110.72 106.96 3.76 1.01e+00 9.80e-01 1.38e+01 ... (remaining 21377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 10106 21.11 - 42.22: 210 42.22 - 63.32: 70 63.32 - 84.43: 33 84.43 - 105.54: 23 Dihedral angle restraints: 10442 sinusoidal: 4922 harmonic: 5520 Sorted by residual: dihedral pdb=" CB CYS C 74 " pdb=" SG CYS C 74 " pdb=" SG CYS E 561 " pdb=" CB CYS E 561 " ideal model delta sinusoidal sigma weight residual 93.00 134.77 -41.77 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA THR G 662 " pdb=" C THR G 662 " pdb=" N LEU G 663 " pdb=" CA LEU G 663 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -122.21 36.21 1 1.00e+01 1.00e-02 1.85e+01 ... (remaining 10439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2424 0.107 - 0.214: 251 0.214 - 0.322: 4 0.322 - 0.429: 1 0.429 - 0.536: 2 Chirality restraints: 2682 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN D 241 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" C1 NAG C 605 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG C 605 " pdb=" O5 NAG C 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" C1 NAG D 606 " pdb=" ND2 ASN D 289 " pdb=" C2 NAG D 606 " pdb=" O5 NAG D 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 2679 not shown) Planarity restraints: 2699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 640 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ASN F 640 " 0.068 2.00e-02 2.50e+03 pdb=" O ASN F 640 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU F 641 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 480 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ARG D 480 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG D 480 " -0.025 2.00e-02 2.50e+03 pdb=" N SER D 481 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 578 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ALA F 578 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA F 578 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG F 579 " 0.022 2.00e-02 2.50e+03 ... (remaining 2696 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2823 2.78 - 3.31: 14008 3.31 - 3.84: 25188 3.84 - 4.37: 29886 4.37 - 4.90: 50846 Nonbonded interactions: 122751 Sorted by model distance: nonbonded pdb=" OD1 ASP D 107 " pdb=" NZ LYS F 574 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASN A 276 " pdb=" OG1 THR A 278 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 432 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP C 113 " pdb=" NZ LYS C 432 " model vdw 2.283 3.120 nonbonded pdb=" OE2 GLU A 293 " pdb=" NZ LYS A 337 " model vdw 2.300 3.120 ... (remaining 122746 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 35 through 501 or resid 601 through 609)) selection = (chain 'C' and (resid 35 through 150 or resid 154 through 398 or resid 414 throu \ gh 501 or resid 605 through 613)) selection = (chain 'D' and (resid 35 through 150 or resid 154 through 398 or resid 414 throu \ gh 501 or resid 602 through 610)) } ncs_group { reference = chain 'B' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'F' and resid 521 through 664) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'S' } 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: 4.710 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.700 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 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: 0.7339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 15824 Z= 0.235 Angle : 1.027 9.526 21682 Z= 0.557 Chirality : 0.062 0.536 2682 Planarity : 0.006 0.044 2644 Dihedral : 11.816 105.538 6744 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.51 (0.19), residues: 1640 helix: -0.04 (0.23), residues: 394 sheet: 0.96 (0.22), residues: 470 loop : 0.30 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 192 TYR 0.020 0.003 TYR F 638 PHE 0.026 0.003 PHE A 233 TRP 0.034 0.004 TRP F 614 HIS 0.009 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00531 (15712) covalent geometry : angle 0.99887 (21382) SS BOND : bond 0.00367 ( 36) SS BOND : angle 1.84107 ( 72) hydrogen bonds : bond 0.14403 ( 481) hydrogen bonds : angle 7.33324 ( 1335) link_ALPHA1-3 : bond 0.00626 ( 3) link_ALPHA1-3 : angle 3.78997 ( 9) link_ALPHA1-6 : bond 0.00789 ( 3) link_ALPHA1-6 : angle 1.15323 ( 9) link_BETA1-4 : bond 0.00636 ( 15) link_BETA1-4 : angle 2.04019 ( 45) link_NAG-ASN : bond 0.00513 ( 55) link_NAG-ASN : angle 2.41551 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.5096 (ptm) cc_final: 0.4838 (ptp) REVERT: A 96 TRP cc_start: 0.7127 (m100) cc_final: 0.6699 (m100) REVERT: A 232 THR cc_start: 0.7035 (p) cc_final: 0.6822 (p) REVERT: A 325 ASN cc_start: 0.7708 (m-40) cc_final: 0.7451 (m110) REVERT: A 449 ILE cc_start: 0.6520 (mt) cc_final: 0.6259 (tt) REVERT: G 539 VAL cc_start: 0.8317 (t) cc_final: 0.8067 (p) REVERT: G 542 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.6973 (mmm160) REVERT: G 595 ILE cc_start: 0.7945 (tp) cc_final: 0.7499 (pt) REVERT: G 641 LEU cc_start: 0.6353 (mt) cc_final: 0.6066 (mp) REVERT: C 99 ASN cc_start: 0.8328 (m-40) cc_final: 0.8074 (t0) REVERT: C 168 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7935 (mmtm) REVERT: C 188 ASN cc_start: 0.7602 (m-40) cc_final: 0.7249 (p0) REVERT: C 356 ASN cc_start: 0.7217 (m-40) cc_final: 0.6840 (t0) REVERT: C 463 ILE cc_start: 0.8832 (pt) cc_final: 0.8596 (mp) REVERT: C 464 THR cc_start: 0.8418 (p) cc_final: 0.8207 (t) REVERT: D 78 ASP cc_start: 0.7742 (m-30) cc_final: 0.7366 (p0) REVERT: D 315 ARG cc_start: 0.7353 (mmt180) cc_final: 0.6824 (mtp-110) REVERT: E 550 GLN cc_start: 0.7758 (tp40) cc_final: 0.7337 (mt0) REVERT: E 634 GLU cc_start: 0.7970 (tp30) cc_final: 0.7747 (tm-30) REVERT: E 636 SER cc_start: 0.8796 (t) cc_final: 0.8315 (p) REVERT: E 639 THR cc_start: 0.8446 (m) cc_final: 0.8061 (p) REVERT: F 641 LEU cc_start: 0.8443 (mt) cc_final: 0.8123 (mt) REVERT: F 644 ASN cc_start: 0.8211 (m-40) cc_final: 0.7521 (m110) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1527 time to fit residues: 62.4245 Evaluate side-chains 155 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS A 363 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS D 363 GLN E 651 ASN F 591 GLN F 616 ASN F 653 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.152301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123302 restraints weight = 25459.770| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.33 r_work: 0.3457 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15824 Z= 0.135 Angle : 0.619 10.041 21682 Z= 0.303 Chirality : 0.046 0.315 2682 Planarity : 0.003 0.029 2644 Dihedral : 8.656 82.672 3571 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.93 % Allowed : 4.94 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.76 (0.20), residues: 1640 helix: 1.11 (0.25), residues: 387 sheet: 0.64 (0.21), residues: 474 loop : 0.24 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 315 TYR 0.012 0.001 TYR G 638 PHE 0.019 0.002 PHE D 53 TRP 0.021 0.002 TRP D 479 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00296 (15712) covalent geometry : angle 0.57653 (21382) SS BOND : bond 0.00246 ( 36) SS BOND : angle 0.72797 ( 72) hydrogen bonds : bond 0.04693 ( 481) hydrogen bonds : angle 5.59494 ( 1335) link_ALPHA1-3 : bond 0.01245 ( 3) link_ALPHA1-3 : angle 2.32197 ( 9) link_ALPHA1-6 : bond 0.00506 ( 3) link_ALPHA1-6 : angle 1.77757 ( 9) link_BETA1-4 : bond 0.00479 ( 15) link_BETA1-4 : angle 1.84806 ( 45) link_NAG-ASN : bond 0.00453 ( 55) link_NAG-ASN : angle 2.38000 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.5386 (ptm) cc_final: 0.5069 (ptp) REVERT: A 96 TRP cc_start: 0.7157 (m100) cc_final: 0.6883 (m100) REVERT: G 542 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7020 (mmm160) REVERT: G 574 LYS cc_start: 0.8281 (tttm) cc_final: 0.7311 (pttm) REVERT: G 633 LYS cc_start: 0.8428 (mttt) cc_final: 0.7844 (mmtt) REVERT: C 188 ASN cc_start: 0.7607 (m-40) cc_final: 0.7303 (p0) REVERT: C 207 LYS cc_start: 0.6491 (tptt) cc_final: 0.5990 (tptp) REVERT: C 356 ASN cc_start: 0.7231 (m-40) cc_final: 0.6879 (t0) REVERT: C 463 ILE cc_start: 0.8866 (pt) cc_final: 0.8519 (mp) REVERT: D 166 ARG cc_start: 0.7099 (mmt-90) cc_final: 0.6894 (mmt-90) REVERT: E 636 SER cc_start: 0.8953 (t) cc_final: 0.8641 (p) REVERT: E 639 THR cc_start: 0.8796 (m) cc_final: 0.8444 (p) REVERT: F 632 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8102 (tp30) outliers start: 14 outliers final: 10 residues processed: 175 average time/residue: 0.1452 time to fit residues: 36.9198 Evaluate side-chains 142 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain G residue 638 TYR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 6 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN G 651 ASN D 99 ASN E 651 ASN F 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.146647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.116263 restraints weight = 25700.360| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.71 r_work: 0.3323 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15824 Z= 0.244 Angle : 0.692 9.447 21682 Z= 0.339 Chirality : 0.049 0.355 2682 Planarity : 0.004 0.036 2644 Dihedral : 8.076 74.559 3571 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.53 % Allowed : 5.67 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.32 (0.20), residues: 1640 helix: 0.98 (0.26), residues: 390 sheet: 0.34 (0.23), residues: 459 loop : -0.15 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 354 TYR 0.016 0.002 TYR G 638 PHE 0.018 0.003 PHE D 53 TRP 0.017 0.002 TRP D 35 HIS 0.006 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00582 (15712) covalent geometry : angle 0.65342 (21382) SS BOND : bond 0.00507 ( 36) SS BOND : angle 1.08231 ( 72) hydrogen bonds : bond 0.04807 ( 481) hydrogen bonds : angle 5.38487 ( 1335) link_ALPHA1-3 : bond 0.01118 ( 3) link_ALPHA1-3 : angle 2.04553 ( 9) link_ALPHA1-6 : bond 0.00645 ( 3) link_ALPHA1-6 : angle 1.71040 ( 9) link_BETA1-4 : bond 0.00441 ( 15) link_BETA1-4 : angle 1.95488 ( 45) link_NAG-ASN : bond 0.00509 ( 55) link_NAG-ASN : angle 2.36308 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.5748 (ptm) cc_final: 0.4991 (tpt) REVERT: A 442 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: G 542 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.6991 (mmm160) REVERT: G 574 LYS cc_start: 0.8339 (tttm) cc_final: 0.7386 (pttm) REVERT: G 577 GLN cc_start: 0.8387 (tt0) cc_final: 0.8137 (tt0) REVERT: C 188 ASN cc_start: 0.7782 (m-40) cc_final: 0.7370 (p0) REVERT: C 207 LYS cc_start: 0.6670 (tptt) cc_final: 0.5785 (tptp) REVERT: C 356 ASN cc_start: 0.7266 (m-40) cc_final: 0.6982 (t0) REVERT: D 166 ARG cc_start: 0.7239 (mmt-90) cc_final: 0.6895 (mmt-90) REVERT: D 432 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8264 (tmtt) REVERT: E 636 SER cc_start: 0.9015 (t) cc_final: 0.8748 (p) REVERT: E 639 THR cc_start: 0.8806 (m) cc_final: 0.8543 (p) REVERT: F 535 MET cc_start: 0.8635 (mpp) cc_final: 0.8266 (mpp) REVERT: F 632 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8053 (tp30) REVERT: F 638 TYR cc_start: 0.7802 (m-80) cc_final: 0.7439 (m-10) REVERT: F 644 ASN cc_start: 0.8358 (m-40) cc_final: 0.7915 (m-40) outliers start: 23 outliers final: 13 residues processed: 163 average time/residue: 0.1448 time to fit residues: 34.4552 Evaluate side-chains 145 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain G residue 638 TYR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 651 ASN Chi-restraints excluded: chain F residue 528 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 148 optimal weight: 0.0020 chunk 136 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.0030 chunk 48 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN F 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.146780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117095 restraints weight = 25545.759| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.68 r_work: 0.3350 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15824 Z= 0.157 Angle : 0.590 9.873 21682 Z= 0.287 Chirality : 0.046 0.294 2682 Planarity : 0.003 0.030 2644 Dihedral : 7.394 71.012 3571 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.20 % Allowed : 7.34 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.16 (0.20), residues: 1640 helix: 1.11 (0.26), residues: 389 sheet: 0.11 (0.23), residues: 455 loop : -0.31 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 354 TYR 0.015 0.001 TYR G 638 PHE 0.018 0.002 PHE D 53 TRP 0.017 0.001 TRP D 479 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00364 (15712) covalent geometry : angle 0.55098 (21382) SS BOND : bond 0.00355 ( 36) SS BOND : angle 0.97012 ( 72) hydrogen bonds : bond 0.04195 ( 481) hydrogen bonds : angle 5.15062 ( 1335) link_ALPHA1-3 : bond 0.01233 ( 3) link_ALPHA1-3 : angle 1.81252 ( 9) link_ALPHA1-6 : bond 0.00786 ( 3) link_ALPHA1-6 : angle 1.72489 ( 9) link_BETA1-4 : bond 0.00438 ( 15) link_BETA1-4 : angle 1.72576 ( 45) link_NAG-ASN : bond 0.00418 ( 55) link_NAG-ASN : angle 2.20374 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.4759 (tp30) cc_final: 0.4420 (tp30) REVERT: A 442 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: A 449 ILE cc_start: 0.6672 (mp) cc_final: 0.6144 (tt) REVERT: G 542 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.6967 (mmm160) REVERT: G 577 GLN cc_start: 0.8321 (tt0) cc_final: 0.8074 (tt0) REVERT: C 188 ASN cc_start: 0.7668 (m-40) cc_final: 0.7251 (p0) REVERT: C 356 ASN cc_start: 0.7261 (m-40) cc_final: 0.6985 (t0) REVERT: E 636 SER cc_start: 0.9001 (t) cc_final: 0.8748 (p) REVERT: E 639 THR cc_start: 0.8762 (m) cc_final: 0.8472 (p) REVERT: E 658 THR cc_start: 0.7841 (p) cc_final: 0.7614 (m) REVERT: F 535 MET cc_start: 0.8604 (mpp) cc_final: 0.8279 (mpp) REVERT: F 542 ARG cc_start: 0.8538 (ptm160) cc_final: 0.7973 (ptm160) REVERT: F 574 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8175 (ttmm) REVERT: F 632 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8009 (tp30) REVERT: F 638 TYR cc_start: 0.7890 (m-80) cc_final: 0.7540 (m-10) REVERT: F 644 ASN cc_start: 0.8367 (m-40) cc_final: 0.7872 (m-40) outliers start: 18 outliers final: 11 residues processed: 144 average time/residue: 0.1314 time to fit residues: 28.6714 Evaluate side-chains 143 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain G residue 638 TYR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 599 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 162 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 148 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 651 ASN F 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.146169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116709 restraints weight = 25620.592| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.71 r_work: 0.3329 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15824 Z= 0.179 Angle : 0.597 9.622 21682 Z= 0.289 Chirality : 0.046 0.308 2682 Planarity : 0.003 0.029 2644 Dihedral : 6.880 71.139 3571 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.27 % Allowed : 7.54 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.20), residues: 1640 helix: 1.03 (0.26), residues: 397 sheet: -0.05 (0.23), residues: 460 loop : -0.41 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.014 0.001 TYR G 638 PHE 0.019 0.002 PHE D 53 TRP 0.018 0.002 TRP D 35 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00422 (15712) covalent geometry : angle 0.56040 (21382) SS BOND : bond 0.00340 ( 36) SS BOND : angle 0.80904 ( 72) hydrogen bonds : bond 0.04148 ( 481) hydrogen bonds : angle 5.07526 ( 1335) link_ALPHA1-3 : bond 0.01212 ( 3) link_ALPHA1-3 : angle 1.74816 ( 9) link_ALPHA1-6 : bond 0.00917 ( 3) link_ALPHA1-6 : angle 1.70983 ( 9) link_BETA1-4 : bond 0.00443 ( 15) link_BETA1-4 : angle 1.69151 ( 45) link_NAG-ASN : bond 0.00419 ( 55) link_NAG-ASN : angle 2.16303 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.4856 (tp30) cc_final: 0.4540 (tp30) REVERT: A 113 ASP cc_start: 0.8169 (t0) cc_final: 0.7961 (t0) REVERT: A 442 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: A 449 ILE cc_start: 0.6728 (mp) cc_final: 0.6262 (tt) REVERT: G 542 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7027 (mmm160) REVERT: G 577 GLN cc_start: 0.8368 (tt0) cc_final: 0.8122 (tt0) REVERT: C 188 ASN cc_start: 0.7665 (m-40) cc_final: 0.7214 (p0) REVERT: C 205 CYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6474 (m) REVERT: C 207 LYS cc_start: 0.6806 (tptt) cc_final: 0.6043 (tptp) REVERT: C 356 ASN cc_start: 0.7273 (m-40) cc_final: 0.6976 (t0) REVERT: D 432 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8290 (tmtt) REVERT: E 636 SER cc_start: 0.8997 (t) cc_final: 0.8749 (p) REVERT: E 639 THR cc_start: 0.8799 (m) cc_final: 0.8513 (p) REVERT: F 542 ARG cc_start: 0.8569 (ptm160) cc_final: 0.7977 (ptm160) REVERT: F 574 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8174 (ttmm) REVERT: F 632 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8068 (tp30) REVERT: F 638 TYR cc_start: 0.7949 (m-80) cc_final: 0.7666 (m-10) REVERT: F 644 ASN cc_start: 0.8424 (m-40) cc_final: 0.7943 (m-40) outliers start: 19 outliers final: 13 residues processed: 157 average time/residue: 0.1314 time to fit residues: 31.0184 Evaluate side-chains 148 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain G residue 638 TYR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 599 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 0.0270 chunk 109 optimal weight: 0.3980 chunk 33 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 105 optimal weight: 0.4980 chunk 143 optimal weight: 3.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 651 ASN F 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.119265 restraints weight = 25402.008| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.47 r_work: 0.3382 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15824 Z= 0.107 Angle : 0.526 9.440 21682 Z= 0.256 Chirality : 0.044 0.296 2682 Planarity : 0.003 0.029 2644 Dihedral : 6.233 72.615 3571 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.20 % Allowed : 8.47 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.07 (0.20), residues: 1640 helix: 1.31 (0.27), residues: 394 sheet: 0.03 (0.23), residues: 459 loop : -0.52 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.014 0.001 TYR G 638 PHE 0.019 0.001 PHE D 53 TRP 0.017 0.001 TRP C 479 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00235 (15712) covalent geometry : angle 0.49208 (21382) SS BOND : bond 0.00209 ( 36) SS BOND : angle 0.64231 ( 72) hydrogen bonds : bond 0.03665 ( 481) hydrogen bonds : angle 4.90601 ( 1335) link_ALPHA1-3 : bond 0.01297 ( 3) link_ALPHA1-3 : angle 1.51634 ( 9) link_ALPHA1-6 : bond 0.00939 ( 3) link_ALPHA1-6 : angle 1.78826 ( 9) link_BETA1-4 : bond 0.00459 ( 15) link_BETA1-4 : angle 1.48647 ( 45) link_NAG-ASN : bond 0.00374 ( 55) link_NAG-ASN : angle 1.98596 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.4783 (tp30) cc_final: 0.4514 (tp30) REVERT: A 442 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: G 542 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.6942 (mmm160) REVERT: G 577 GLN cc_start: 0.8293 (tt0) cc_final: 0.8047 (tt0) REVERT: G 647 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6123 (mt-10) REVERT: C 188 ASN cc_start: 0.7581 (m-40) cc_final: 0.7138 (p0) REVERT: C 207 LYS cc_start: 0.6799 (tptt) cc_final: 0.6141 (tptp) REVERT: C 475 MET cc_start: 0.8517 (tpp) cc_final: 0.8271 (tpp) REVERT: E 636 SER cc_start: 0.8965 (t) cc_final: 0.8749 (p) REVERT: E 639 THR cc_start: 0.8703 (m) cc_final: 0.8406 (p) REVERT: F 535 MET cc_start: 0.8532 (mpp) cc_final: 0.8314 (mpp) REVERT: F 542 ARG cc_start: 0.8589 (ptm160) cc_final: 0.7856 (ptm160) REVERT: F 574 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8178 (ttmm) REVERT: F 632 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8018 (tp30) REVERT: F 644 ASN cc_start: 0.8418 (m-40) cc_final: 0.7898 (m-40) outliers start: 18 outliers final: 12 residues processed: 150 average time/residue: 0.1318 time to fit residues: 29.9289 Evaluate side-chains 143 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain G residue 638 TYR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 599 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117124 restraints weight = 25344.295| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.65 r_work: 0.3334 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15824 Z= 0.167 Angle : 0.578 9.070 21682 Z= 0.279 Chirality : 0.045 0.307 2682 Planarity : 0.003 0.030 2644 Dihedral : 6.189 70.900 3571 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.00 % Allowed : 9.41 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.01 (0.20), residues: 1640 helix: 1.22 (0.27), residues: 400 sheet: -0.12 (0.23), residues: 452 loop : -0.49 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 480 TYR 0.013 0.001 TYR G 638 PHE 0.016 0.002 PHE D 53 TRP 0.014 0.001 TRP F 610 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00396 (15712) covalent geometry : angle 0.54267 (21382) SS BOND : bond 0.00356 ( 36) SS BOND : angle 0.89636 ( 72) hydrogen bonds : bond 0.04006 ( 481) hydrogen bonds : angle 4.94393 ( 1335) link_ALPHA1-3 : bond 0.01220 ( 3) link_ALPHA1-3 : angle 1.62592 ( 9) link_ALPHA1-6 : bond 0.00851 ( 3) link_ALPHA1-6 : angle 1.73926 ( 9) link_BETA1-4 : bond 0.00441 ( 15) link_BETA1-4 : angle 1.64851 ( 45) link_NAG-ASN : bond 0.00386 ( 55) link_NAG-ASN : angle 2.06628 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.4872 (tp30) cc_final: 0.4564 (tp30) REVERT: A 373 MET cc_start: 0.7260 (mtm) cc_final: 0.6411 (mtm) REVERT: A 449 ILE cc_start: 0.6863 (mp) cc_final: 0.6423 (tt) REVERT: G 542 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.6960 (mmm160) REVERT: G 577 GLN cc_start: 0.8347 (tt0) cc_final: 0.8093 (tt0) REVERT: C 188 ASN cc_start: 0.7647 (m-40) cc_final: 0.7210 (p0) REVERT: C 207 LYS cc_start: 0.6805 (tptt) cc_final: 0.6483 (tptt) REVERT: C 475 MET cc_start: 0.8577 (tpp) cc_final: 0.8328 (tpp) REVERT: E 636 SER cc_start: 0.9024 (t) cc_final: 0.8797 (p) REVERT: E 639 THR cc_start: 0.8756 (m) cc_final: 0.8427 (p) REVERT: F 535 MET cc_start: 0.8512 (mpp) cc_final: 0.8277 (mpp) REVERT: F 542 ARG cc_start: 0.8581 (ptm160) cc_final: 0.7838 (ptm160) REVERT: F 574 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8228 (ttmm) REVERT: F 632 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8304 (tm-30) REVERT: F 644 ASN cc_start: 0.8457 (m-40) cc_final: 0.7955 (m-40) outliers start: 15 outliers final: 13 residues processed: 142 average time/residue: 0.1283 time to fit residues: 27.7613 Evaluate side-chains 142 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain G residue 638 TYR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 641 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS E 651 ASN F 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116169 restraints weight = 25571.508| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.65 r_work: 0.3324 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15824 Z= 0.192 Angle : 0.601 8.820 21682 Z= 0.291 Chirality : 0.046 0.330 2682 Planarity : 0.003 0.029 2644 Dihedral : 6.016 68.975 3571 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.27 % Allowed : 9.34 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.21 (0.20), residues: 1640 helix: 1.14 (0.27), residues: 400 sheet: -0.35 (0.23), residues: 454 loop : -0.59 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.014 0.001 TYR G 638 PHE 0.016 0.002 PHE D 53 TRP 0.013 0.002 TRP D 479 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00456 (15712) covalent geometry : angle 0.56618 (21382) SS BOND : bond 0.00366 ( 36) SS BOND : angle 0.95595 ( 72) hydrogen bonds : bond 0.04144 ( 481) hydrogen bonds : angle 5.03112 ( 1335) link_ALPHA1-3 : bond 0.01144 ( 3) link_ALPHA1-3 : angle 1.42936 ( 9) link_ALPHA1-6 : bond 0.00773 ( 3) link_ALPHA1-6 : angle 1.44631 ( 9) link_BETA1-4 : bond 0.00475 ( 15) link_BETA1-4 : angle 1.71357 ( 45) link_NAG-ASN : bond 0.00402 ( 55) link_NAG-ASN : angle 2.12181 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.4932 (tp30) cc_final: 0.4636 (tp30) REVERT: A 449 ILE cc_start: 0.7001 (mp) cc_final: 0.6579 (tt) REVERT: G 542 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7007 (mmm160) REVERT: G 577 GLN cc_start: 0.8354 (tt0) cc_final: 0.8098 (tt0) REVERT: C 205 CYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6682 (m) REVERT: C 207 LYS cc_start: 0.6821 (tptt) cc_final: 0.6488 (tptt) REVERT: D 432 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8231 (tmtt) REVERT: E 636 SER cc_start: 0.9063 (t) cc_final: 0.8824 (p) REVERT: E 639 THR cc_start: 0.8807 (m) cc_final: 0.8479 (p) REVERT: F 574 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8272 (ttmm) REVERT: F 644 ASN cc_start: 0.8425 (m-40) cc_final: 0.7913 (m-40) outliers start: 19 outliers final: 14 residues processed: 143 average time/residue: 0.1257 time to fit residues: 27.6267 Evaluate side-chains 142 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain G residue 638 TYR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 641 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 17 optimal weight: 0.0970 chunk 22 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 116 optimal weight: 0.0370 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 651 ASN F 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.147341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.118205 restraints weight = 25253.814| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.33 r_work: 0.3380 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15824 Z= 0.103 Angle : 0.523 9.003 21682 Z= 0.257 Chirality : 0.043 0.300 2682 Planarity : 0.003 0.029 2644 Dihedral : 5.430 71.195 3571 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.07 % Allowed : 9.74 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.20), residues: 1640 helix: 1.40 (0.27), residues: 398 sheet: -0.20 (0.23), residues: 454 loop : -0.53 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.015 0.001 TYR F 638 PHE 0.017 0.001 PHE D 53 TRP 0.019 0.001 TRP C 479 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00223 (15712) covalent geometry : angle 0.49177 (21382) SS BOND : bond 0.00243 ( 36) SS BOND : angle 0.67625 ( 72) hydrogen bonds : bond 0.03605 ( 481) hydrogen bonds : angle 4.81864 ( 1335) link_ALPHA1-3 : bond 0.01144 ( 3) link_ALPHA1-3 : angle 1.22624 ( 9) link_ALPHA1-6 : bond 0.00752 ( 3) link_ALPHA1-6 : angle 1.39738 ( 9) link_BETA1-4 : bond 0.00492 ( 15) link_BETA1-4 : angle 1.47857 ( 45) link_NAG-ASN : bond 0.00344 ( 55) link_NAG-ASN : angle 1.91088 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.4855 (tp30) cc_final: 0.4609 (tp30) REVERT: A 373 MET cc_start: 0.7411 (mtm) cc_final: 0.6831 (mtm) REVERT: G 542 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.6919 (mmm160) REVERT: G 577 GLN cc_start: 0.8269 (tt0) cc_final: 0.8003 (tt0) REVERT: C 82 GLN cc_start: 0.8145 (pp30) cc_final: 0.7796 (pp30) REVERT: C 188 ASN cc_start: 0.7631 (m-40) cc_final: 0.7135 (p0) REVERT: C 205 CYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6634 (m) REVERT: C 207 LYS cc_start: 0.6585 (tptt) cc_final: 0.6184 (tptt) REVERT: C 280 ASN cc_start: 0.8260 (p0) cc_final: 0.7932 (p0) REVERT: E 636 SER cc_start: 0.9002 (t) cc_final: 0.8782 (p) REVERT: E 639 THR cc_start: 0.8705 (m) cc_final: 0.8347 (p) REVERT: E 657 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7451 (mt-10) REVERT: F 574 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8258 (ttmm) REVERT: F 644 ASN cc_start: 0.8369 (m-40) cc_final: 0.7837 (m-40) outliers start: 16 outliers final: 13 residues processed: 138 average time/residue: 0.1259 time to fit residues: 26.8349 Evaluate side-chains 141 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain G residue 638 TYR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 51 optimal weight: 0.0060 chunk 40 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.0060 chunk 115 optimal weight: 0.0370 chunk 128 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 85 optimal weight: 0.0980 overall best weight: 0.2290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 651 ASN F 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.148874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120056 restraints weight = 25363.416| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.32 r_work: 0.3407 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15824 Z= 0.091 Angle : 0.495 8.909 21682 Z= 0.243 Chirality : 0.043 0.296 2682 Planarity : 0.003 0.028 2644 Dihedral : 4.968 72.013 3571 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.87 % Allowed : 9.94 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.20), residues: 1640 helix: 1.52 (0.27), residues: 400 sheet: -0.02 (0.23), residues: 446 loop : -0.46 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.017 0.001 TYR F 638 PHE 0.011 0.001 PHE D 53 TRP 0.016 0.001 TRP C 479 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00193 (15712) covalent geometry : angle 0.46569 (21382) SS BOND : bond 0.00205 ( 36) SS BOND : angle 0.63397 ( 72) hydrogen bonds : bond 0.03411 ( 481) hydrogen bonds : angle 4.68384 ( 1335) link_ALPHA1-3 : bond 0.01064 ( 3) link_ALPHA1-3 : angle 1.18936 ( 9) link_ALPHA1-6 : bond 0.00806 ( 3) link_ALPHA1-6 : angle 1.31745 ( 9) link_BETA1-4 : bond 0.00480 ( 15) link_BETA1-4 : angle 1.43858 ( 45) link_NAG-ASN : bond 0.00319 ( 55) link_NAG-ASN : angle 1.79387 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.4776 (tp30) cc_final: 0.4575 (tp30) REVERT: A 373 MET cc_start: 0.7471 (mtm) cc_final: 0.6820 (mtm) REVERT: G 542 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.6845 (mmm160) REVERT: G 577 GLN cc_start: 0.8219 (tt0) cc_final: 0.7972 (tt0) REVERT: C 82 GLN cc_start: 0.8116 (pp30) cc_final: 0.7722 (pp30) REVERT: C 188 ASN cc_start: 0.7612 (m-40) cc_final: 0.7099 (p0) REVERT: C 205 CYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6554 (m) REVERT: C 207 LYS cc_start: 0.6665 (tptt) cc_final: 0.6108 (tptt) REVERT: C 280 ASN cc_start: 0.8219 (p0) cc_final: 0.7901 (p0) REVERT: E 636 SER cc_start: 0.8986 (t) cc_final: 0.8784 (p) REVERT: E 639 THR cc_start: 0.8658 (m) cc_final: 0.8272 (p) REVERT: E 647 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7202 (mt-10) REVERT: E 657 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7535 (mt-10) REVERT: F 574 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8138 (ttmm) REVERT: F 632 GLU cc_start: 0.8015 (tp30) cc_final: 0.7683 (tm-30) REVERT: F 638 TYR cc_start: 0.7908 (m-80) cc_final: 0.7611 (m-10) REVERT: F 644 ASN cc_start: 0.8335 (m-40) cc_final: 0.7827 (m-40) outliers start: 13 outliers final: 9 residues processed: 141 average time/residue: 0.1296 time to fit residues: 28.0532 Evaluate side-chains 135 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 136 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 113 optimal weight: 0.4980 chunk 3 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN C 356 ASN E 651 ASN F 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.145043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115799 restraints weight = 25299.023| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.59 r_work: 0.3311 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15824 Z= 0.222 Angle : 0.631 8.504 21682 Z= 0.305 Chirality : 0.047 0.332 2682 Planarity : 0.004 0.030 2644 Dihedral : 5.537 67.694 3571 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.00 % Allowed : 9.54 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.21), residues: 1640 helix: 1.32 (0.27), residues: 395 sheet: -0.31 (0.23), residues: 461 loop : -0.52 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 480 TYR 0.018 0.002 TYR F 638 PHE 0.015 0.002 PHE D 53 TRP 0.014 0.002 TRP C 69 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00532 (15712) covalent geometry : angle 0.59976 (21382) SS BOND : bond 0.00408 ( 36) SS BOND : angle 0.99202 ( 72) hydrogen bonds : bond 0.04240 ( 481) hydrogen bonds : angle 4.95006 ( 1335) link_ALPHA1-3 : bond 0.00965 ( 3) link_ALPHA1-3 : angle 1.29642 ( 9) link_ALPHA1-6 : bond 0.00708 ( 3) link_ALPHA1-6 : angle 1.50395 ( 9) link_BETA1-4 : bond 0.00431 ( 15) link_BETA1-4 : angle 1.72013 ( 45) link_NAG-ASN : bond 0.00406 ( 55) link_NAG-ASN : angle 2.06833 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.97 seconds wall clock time: 70 minutes 21.57 seconds (4221.57 seconds total)