Starting phenix.real_space_refine on Thu Feb 5 10:32:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nc8_49242/02_2026/9nc8_49242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nc8_49242/02_2026/9nc8_49242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nc8_49242/02_2026/9nc8_49242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nc8_49242/02_2026/9nc8_49242.map" model { file = "/net/cci-nas-00/data/ceres_data/9nc8_49242/02_2026/9nc8_49242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nc8_49242/02_2026/9nc8_49242.cif" } resolution = 3.55 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= -0.001 sd= 0.030 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 115 5.16 5 C 10306 2.51 5 N 2738 2.21 5 O 3295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16454 Number of models: 1 Model: "" Number of chains: 23 Chain: "E" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3541 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "F" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1116 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 139} Chain breaks: 1 Chain: "A" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3508 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1013 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1013 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1007 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 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 Time building chain proxies: 4.09, per 1000 atoms: 0.25 Number of scatterers: 16454 At special positions: 0 Unit cell: (130.696, 132.804, 133.858, 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 115 16.00 O 3295 8.00 N 2738 7.00 C 10306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.16 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.14 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.13 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.08 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.12 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.18 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.16 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.11 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.11 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 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 D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 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 G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 289 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 356 " " NAG A 607 " - " ASN A 362 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 295 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 88 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 197 " " NAG C 606 " - " ASN C 241 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 301 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 295 " " NAG C 611 " - " ASN C 362 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 448 " " NAG E 601 " - " ASN E 130 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 332 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 356 " " NAG E 609 " - " ASN E 362 " " NAG E 610 " - " ASN E 386 " " NAG E 611 " - " ASN E 392 " " NAG E 612 " - " ASN E 295 " " NAG E 613 " - " ASN E 448 " " NAG E 614 " - " ASN E 289 " " NAG G 1 " - " ASN E 88 " " NAG I 1 " - " ASN E 241 " " NAG J 1 " - " ASN E 262 " " NAG K 1 " - " ASN F 625 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 197 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 448 " " NAG T 1 " - " ASN C 262 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 816.7 milliseconds 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3658 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 26 sheets defined 27.6% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.703A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 396 through 405 removed outlier: 3.619A pdb=" N GLY E 405 " --> pdb=" O THR E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.915A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 528 removed outlier: 3.931A pdb=" N GLY F 524 " --> pdb=" O GLY F 521 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 538 Processing helix chain 'F' and resid 545 through 553 removed outlier: 3.654A pdb=" N GLN F 551 " --> pdb=" O GLY F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 597 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.782A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.612A pdb=" N LEU F 663 " --> pdb=" O GLU F 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.268A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.733A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.657A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.703A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.776A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.737A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.798A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.752A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.511A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.606A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100E through 100I removed outlier: 3.512A pdb=" N PHE H 100I" --> pdb=" O SER H 100F" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.030A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.460A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.908A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.943A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 298 removed outlier: 7.229A pdb=" N VAL E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER E 334 " --> pdb=" O VAL E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 329 through 334 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'E' and resid 303 through 312 removed outlier: 6.975A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE E 309 " --> pdb=" O ARG E 315 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.212A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.542A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.870A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AB5, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.199A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.644A pdb=" N ASN A 301 " --> pdb=" O ILE A 322A" (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.676A 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 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.381A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.543A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.940A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, 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: 6.936A pdb=" N ASN C 301 " --> pdb=" O ILE C 322A" (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE C 322A" --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.855A 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 323 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=AC5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95A through 98 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 19 through 24 519 hydrogen bonds defined for protein. 1395 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: 2.95 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3415 1.33 - 1.45: 4129 1.45 - 1.58: 9062 1.58 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 16765 Sorted by residual: bond pdb=" N PRO E 253 " pdb=" CA PRO E 253 " ideal model delta sigma weight residual 1.469 1.436 0.033 1.22e-02 6.72e+03 7.51e+00 bond pdb=" NE ARG E 456 " pdb=" CZ ARG E 456 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.36e+00 bond pdb=" CG ASP E 180 " pdb=" OD2 ASP E 180 " ideal model delta sigma weight residual 1.249 1.200 0.049 1.90e-02 2.77e+03 6.77e+00 bond pdb=" CD GLU F 654 " pdb=" OE1 GLU F 654 " ideal model delta sigma weight residual 1.249 1.200 0.049 1.90e-02 2.77e+03 6.74e+00 bond pdb=" N PRO A 313 " pdb=" CA PRO A 313 " ideal model delta sigma weight residual 1.468 1.437 0.031 1.20e-02 6.94e+03 6.70e+00 ... (remaining 16760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 20589 2.01 - 4.02: 1823 4.02 - 6.03: 283 6.03 - 8.04: 57 8.04 - 10.05: 6 Bond angle restraints: 22758 Sorted by residual: angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 125.70 -6.04 7.30e-01 1.88e+00 6.84e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 125.66 -6.00 7.30e-01 1.88e+00 6.75e+01 angle pdb=" C THR A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 119.78 127.84 -8.06 1.03e+00 9.43e-01 6.13e+01 angle pdb=" C ARG H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta sigma weight residual 119.85 127.50 -7.65 1.01e+00 9.80e-01 5.74e+01 angle pdb=" C ASP A 368 " pdb=" N PRO A 369 " pdb=" CA PRO A 369 " ideal model delta sigma weight residual 119.47 127.89 -8.42 1.16e+00 7.43e-01 5.27e+01 ... (remaining 22753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 10633 21.98 - 43.95: 229 43.95 - 65.93: 77 65.93 - 87.91: 51 87.91 - 109.89: 26 Dihedral angle restraints: 11016 sinusoidal: 5363 harmonic: 5653 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 42.09 50.91 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -135.07 49.07 1 1.00e+01 1.00e-02 3.31e+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 -126.26 40.26 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 11013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2625 0.131 - 0.262: 150 0.262 - 0.393: 3 0.393 - 0.523: 4 0.523 - 0.654: 2 Chirality restraints: 2784 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-02 2.50e+03 1.07e+03 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-02 2.50e+03 6.92e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-02 2.50e+03 4.52e+02 ... (remaining 2781 not shown) Planarity restraints: 2852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 332 " -0.125 2.00e-02 2.50e+03 1.28e-01 2.05e+02 pdb=" CG ASN C 332 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 332 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN C 332 " 0.194 2.00e-02 2.50e+03 pdb=" C1 NAG C 609 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 241 " 0.085 2.00e-02 2.50e+03 9.10e-02 1.03e+02 pdb=" CG ASN C 241 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 241 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 241 " -0.146 2.00e-02 2.50e+03 pdb=" C1 NAG C 606 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 295 " 0.060 2.00e-02 2.50e+03 6.22e-02 4.84e+01 pdb=" CG ASN A 295 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 295 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 295 " -0.097 2.00e-02 2.50e+03 pdb=" C1 NAG A 609 " 0.074 2.00e-02 2.50e+03 ... (remaining 2849 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 4876 2.82 - 3.34: 14495 3.34 - 3.86: 27181 3.86 - 4.38: 31027 4.38 - 4.90: 52475 Nonbonded interactions: 130054 Sorted by model distance: nonbonded pdb=" O3 NAG N 1 " pdb=" O5 NAG N 2 " model vdw 2.306 3.040 nonbonded pdb=" N ASN C 197 " pdb=" OD1 ASN C 197 " model vdw 2.341 3.120 nonbonded pdb=" OG1 THR A 163 " pdb=" O ILE A 165 " model vdw 2.357 3.040 nonbonded pdb=" O3 NAG G 1 " pdb=" O5 NAG G 2 " model vdw 2.436 3.040 nonbonded pdb=" O4 NAG C 607 " pdb=" O6 NAG C 607 " model vdw 2.439 3.040 ... (remaining 130049 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 32 through 56 or resid 67 through 132 or resid 153 through \ 184 or resid 189 through 609)) selection = (chain 'C' and (resid 32 through 56 or resid 67 through 132 or resid 153 through \ 609)) selection = (chain 'E' and (resid 32 through 56 or resid 67 through 184 or resid 189 through \ 609)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and (resid 518 through 546 or resid 568 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2)))) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.150 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 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 : 0.013 0.147 16871 Z= 0.672 Angle : 1.296 14.680 23041 Z= 0.820 Chirality : 0.073 0.654 2784 Planarity : 0.005 0.023 2804 Dihedral : 13.118 109.885 7253 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.17 % Allowed : 0.92 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.18), residues: 1923 helix: 0.48 (0.21), residues: 433 sheet: 1.74 (0.21), residues: 522 loop : 2.97 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.028 0.004 TYR H 33 PHE 0.020 0.004 PHE C 317 TRP 0.029 0.005 TRP E 427 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.01176 (16765) covalent geometry : angle 1.25782 (22758) SS BOND : bond 0.05480 ( 35) SS BOND : angle 3.41104 ( 70) hydrogen bonds : bond 0.20903 ( 519) hydrogen bonds : angle 7.11744 ( 1395) link_ALPHA1-3 : bond 0.00640 ( 5) link_ALPHA1-3 : angle 2.98332 ( 15) link_BETA1-4 : bond 0.00532 ( 18) link_BETA1-4 : angle 2.68875 ( 54) link_NAG-ASN : bond 0.06984 ( 48) link_NAG-ASN : angle 3.08793 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 466 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 VAL cc_start: 0.6348 (p) cc_final: 0.6121 (m) REVERT: E 209 THR cc_start: 0.7099 (m) cc_final: 0.6897 (p) REVERT: E 363 GLN cc_start: 0.6092 (pm20) cc_final: 0.5866 (tp40) REVERT: E 463 ASN cc_start: 0.7379 (m-40) cc_final: 0.6873 (t0) REVERT: A 192 ARG cc_start: 0.7242 (mtt180) cc_final: 0.6945 (mtm-85) REVERT: A 377 ASN cc_start: 0.7769 (t0) cc_final: 0.7454 (p0) REVERT: A 434 MET cc_start: 0.7794 (tmm) cc_final: 0.7501 (ttt) REVERT: A 435 TYR cc_start: 0.7067 (t80) cc_final: 0.6413 (t80) REVERT: A 491 ILE cc_start: 0.8459 (mt) cc_final: 0.8217 (mm) REVERT: B 530 MET cc_start: 0.6503 (mtp) cc_final: 0.6253 (mtp) REVERT: B 654 GLU cc_start: 0.7320 (tt0) cc_final: 0.7032 (tt0) REVERT: C 332 ASN cc_start: 0.7081 (m-40) cc_final: 0.6806 (p0) REVERT: D 628 TRP cc_start: 0.5582 (m100) cc_final: 0.5166 (m100) REVERT: D 654 GLU cc_start: 0.6567 (mt-10) cc_final: 0.6290 (tp30) REVERT: H 11 MET cc_start: 0.7384 (ttm) cc_final: 0.7169 (pmm) REVERT: H 100 TYR cc_start: 0.6048 (m-80) cc_final: 0.5795 (m-80) REVERT: L 39 HIS cc_start: 0.6668 (t-90) cc_final: 0.6421 (t70) REVERT: L 40 PRO cc_start: 0.7094 (Cg_exo) cc_final: 0.6861 (Cg_endo) REVERT: L 46 LEU cc_start: 0.6159 (tp) cc_final: 0.5799 (tp) outliers start: 3 outliers final: 1 residues processed: 468 average time/residue: 0.1543 time to fit residues: 103.9766 Evaluate side-chains 201 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 374 HIS ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN C 246 GLN C 302 ASN H 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.152233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.136939 restraints weight = 38761.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.139828 restraints weight = 22988.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.141762 restraints weight = 15589.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.143105 restraints weight = 11669.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.144019 restraints weight = 9345.072| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16871 Z= 0.170 Angle : 0.709 11.576 23041 Z= 0.359 Chirality : 0.048 0.242 2784 Planarity : 0.004 0.032 2804 Dihedral : 9.362 76.681 3558 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.46 % Allowed : 8.71 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.19), residues: 1923 helix: 1.64 (0.23), residues: 432 sheet: 1.17 (0.21), residues: 535 loop : 2.09 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 633 TYR 0.018 0.002 TYR D 643 PHE 0.019 0.002 PHE B 522 TRP 0.040 0.002 TRP A 395 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00376 (16765) covalent geometry : angle 0.67646 (22758) SS BOND : bond 0.00447 ( 35) SS BOND : angle 1.38254 ( 70) hydrogen bonds : bond 0.05963 ( 519) hydrogen bonds : angle 5.70025 ( 1395) link_ALPHA1-3 : bond 0.01530 ( 5) link_ALPHA1-3 : angle 1.93090 ( 15) link_BETA1-4 : bond 0.00606 ( 18) link_BETA1-4 : angle 1.90585 ( 54) link_NAG-ASN : bond 0.00329 ( 48) link_NAG-ASN : angle 2.34685 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 391 PHE cc_start: 0.5442 (m-80) cc_final: 0.4771 (m-80) REVERT: A 377 ASN cc_start: 0.7661 (t0) cc_final: 0.7354 (p0) REVERT: A 434 MET cc_start: 0.7744 (tmm) cc_final: 0.7314 (ttp) REVERT: A 491 ILE cc_start: 0.8372 (mt) cc_final: 0.8047 (mm) REVERT: B 575 GLN cc_start: 0.8078 (pp30) cc_final: 0.7669 (pp30) REVERT: C 272 ILE cc_start: 0.6934 (tp) cc_final: 0.6589 (pt) REVERT: C 373 MET cc_start: 0.7466 (mtp) cc_final: 0.7143 (mtp) REVERT: C 484 TYR cc_start: 0.6721 (p90) cc_final: 0.6414 (p90) REVERT: D 601 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7441 (ptmt) REVERT: H 100 TYR cc_start: 0.5947 (m-80) cc_final: 0.5646 (m-80) outliers start: 43 outliers final: 21 residues processed: 264 average time/residue: 0.1281 time to fit residues: 52.5450 Evaluate side-chains 182 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 91 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 170 GLN E 374 HIS ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 302 ASN H 6 GLN H 35 HIS H 39 GLN H 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.149645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.133207 restraints weight = 39801.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.136042 restraints weight = 24699.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.137929 restraints weight = 17382.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.139248 restraints weight = 13453.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.140163 restraints weight = 11083.055| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16871 Z= 0.180 Angle : 0.681 10.800 23041 Z= 0.343 Chirality : 0.047 0.233 2784 Planarity : 0.004 0.035 2804 Dihedral : 7.769 59.451 3556 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.58 % Allowed : 10.77 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.18), residues: 1923 helix: 1.84 (0.24), residues: 432 sheet: 0.99 (0.21), residues: 502 loop : 1.55 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 633 TYR 0.015 0.002 TYR C 484 PHE 0.022 0.002 PHE E 361 TRP 0.015 0.002 TRP B 628 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00407 (16765) covalent geometry : angle 0.65137 (22758) SS BOND : bond 0.00467 ( 35) SS BOND : angle 1.49054 ( 70) hydrogen bonds : bond 0.05151 ( 519) hydrogen bonds : angle 5.45391 ( 1395) link_ALPHA1-3 : bond 0.01303 ( 5) link_ALPHA1-3 : angle 1.54061 ( 15) link_BETA1-4 : bond 0.00525 ( 18) link_BETA1-4 : angle 1.53601 ( 54) link_NAG-ASN : bond 0.00455 ( 48) link_NAG-ASN : angle 2.19879 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.6786 (p0) cc_final: 0.6323 (t0) REVERT: A 377 ASN cc_start: 0.7779 (t0) cc_final: 0.7478 (p0) REVERT: A 426 MET cc_start: 0.7726 (mtm) cc_final: 0.7333 (mpp) REVERT: A 434 MET cc_start: 0.7821 (tmm) cc_final: 0.7289 (ttp) REVERT: A 491 ILE cc_start: 0.8477 (mt) cc_final: 0.8179 (mm) REVERT: B 575 GLN cc_start: 0.8056 (pp30) cc_final: 0.7635 (pp30) REVERT: C 272 ILE cc_start: 0.6895 (tp) cc_final: 0.6596 (pt) REVERT: C 389 LYS cc_start: 0.7275 (mttt) cc_final: 0.6612 (mttm) REVERT: D 601 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7508 (ptmt) REVERT: D 629 MET cc_start: 0.2329 (mmm) cc_final: 0.2118 (mmm) REVERT: L 38 GLN cc_start: 0.6882 (tt0) cc_final: 0.6644 (pp30) outliers start: 45 outliers final: 26 residues processed: 217 average time/residue: 0.1255 time to fit residues: 42.5046 Evaluate side-chains 182 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 0.0670 chunk 184 optimal weight: 10.0000 chunk 185 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 HIS F 550 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN C 229 ASN D 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.149451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.134181 restraints weight = 38755.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.137008 restraints weight = 23014.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.138944 restraints weight = 15712.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.140251 restraints weight = 11817.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.141185 restraints weight = 9559.763| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16871 Z= 0.122 Angle : 0.601 10.928 23041 Z= 0.300 Chirality : 0.045 0.214 2784 Planarity : 0.003 0.039 2804 Dihedral : 6.589 47.544 3556 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.83 % Allowed : 11.81 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.19), residues: 1923 helix: 1.99 (0.25), residues: 433 sheet: 0.79 (0.21), residues: 525 loop : 1.45 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 588 TYR 0.017 0.001 TYR C 435 PHE 0.013 0.001 PHE C 53 TRP 0.015 0.001 TRP B 628 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00266 (16765) covalent geometry : angle 0.57217 (22758) SS BOND : bond 0.00550 ( 35) SS BOND : angle 1.26703 ( 70) hydrogen bonds : bond 0.04396 ( 519) hydrogen bonds : angle 5.15707 ( 1395) link_ALPHA1-3 : bond 0.01380 ( 5) link_ALPHA1-3 : angle 1.56231 ( 15) link_BETA1-4 : bond 0.00537 ( 18) link_BETA1-4 : angle 1.46902 ( 54) link_NAG-ASN : bond 0.00310 ( 48) link_NAG-ASN : angle 2.06311 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 373 MET cc_start: 0.6576 (mmm) cc_final: 0.6248 (ttm) REVERT: A 377 ASN cc_start: 0.7760 (t0) cc_final: 0.7429 (p0) REVERT: A 426 MET cc_start: 0.7537 (mtm) cc_final: 0.7200 (mpp) REVERT: A 491 ILE cc_start: 0.8394 (mt) cc_final: 0.8127 (mm) REVERT: B 575 GLN cc_start: 0.8007 (pp30) cc_final: 0.7605 (pp30) REVERT: C 111 LEU cc_start: 0.8036 (mt) cc_final: 0.7671 (mt) REVERT: C 272 ILE cc_start: 0.6815 (tp) cc_final: 0.6573 (pt) REVERT: C 389 LYS cc_start: 0.7271 (mttt) cc_final: 0.6627 (mttm) REVERT: H 52 ASN cc_start: 0.6992 (t0) cc_final: 0.6335 (t0) outliers start: 32 outliers final: 18 residues processed: 211 average time/residue: 0.1241 time to fit residues: 41.1477 Evaluate side-chains 176 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 14 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 249 HIS E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.147075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.131269 restraints weight = 38952.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.134101 restraints weight = 23142.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.136018 restraints weight = 15887.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.137350 restraints weight = 12036.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.138283 restraints weight = 9768.997| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16871 Z= 0.152 Angle : 0.608 9.099 23041 Z= 0.305 Chirality : 0.046 0.201 2784 Planarity : 0.004 0.048 2804 Dihedral : 5.932 41.998 3556 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.81 % Allowed : 11.52 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.18), residues: 1923 helix: 1.94 (0.25), residues: 433 sheet: 0.84 (0.21), residues: 494 loop : 1.16 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 633 TYR 0.012 0.002 TYR C 435 PHE 0.018 0.002 PHE E 361 TRP 0.018 0.002 TRP B 628 HIS 0.006 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00349 (16765) covalent geometry : angle 0.58025 (22758) SS BOND : bond 0.00354 ( 35) SS BOND : angle 1.21084 ( 70) hydrogen bonds : bond 0.04312 ( 519) hydrogen bonds : angle 5.08599 ( 1395) link_ALPHA1-3 : bond 0.01267 ( 5) link_ALPHA1-3 : angle 1.57796 ( 15) link_BETA1-4 : bond 0.00470 ( 18) link_BETA1-4 : angle 1.43048 ( 54) link_NAG-ASN : bond 0.00243 ( 48) link_NAG-ASN : angle 2.07240 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.7761 (t0) cc_final: 0.7357 (p0) REVERT: A 456 ARG cc_start: 0.6912 (ttp-170) cc_final: 0.6635 (ptm-80) REVERT: A 491 ILE cc_start: 0.8439 (mt) cc_final: 0.8163 (mm) REVERT: B 575 GLN cc_start: 0.8130 (pp30) cc_final: 0.7721 (pp30) REVERT: C 95 MET cc_start: 0.7545 (mtm) cc_final: 0.7204 (mtm) REVERT: C 111 LEU cc_start: 0.8117 (mt) cc_final: 0.7784 (mt) REVERT: C 272 ILE cc_start: 0.6871 (tp) cc_final: 0.6590 (pt) REVERT: C 389 LYS cc_start: 0.7514 (mttt) cc_final: 0.7151 (ttmt) REVERT: C 484 TYR cc_start: 0.7051 (p90) cc_final: 0.6688 (p90) REVERT: L 39 HIS cc_start: 0.6147 (OUTLIER) cc_final: 0.5640 (m-70) outliers start: 49 outliers final: 34 residues processed: 201 average time/residue: 0.1201 time to fit residues: 38.0278 Evaluate side-chains 186 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 656 ASN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 39 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 9 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN L 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.132375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.116339 restraints weight = 39769.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.118981 restraints weight = 24444.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.120801 restraints weight = 17225.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.122066 restraints weight = 13311.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122966 restraints weight = 10996.749| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16871 Z= 0.243 Angle : 0.739 8.933 23041 Z= 0.372 Chirality : 0.050 0.245 2784 Planarity : 0.005 0.064 2804 Dihedral : 6.172 47.056 3556 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.81 % Allowed : 12.21 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 1923 helix: 1.42 (0.25), residues: 436 sheet: 0.35 (0.22), residues: 479 loop : 0.61 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 633 TYR 0.017 0.002 TYR L 36 PHE 0.027 0.003 PHE E 361 TRP 0.036 0.002 TRP B 623 HIS 0.008 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00566 (16765) covalent geometry : angle 0.70844 (22758) SS BOND : bond 0.00538 ( 35) SS BOND : angle 1.58035 ( 70) hydrogen bonds : bond 0.04991 ( 519) hydrogen bonds : angle 5.52827 ( 1395) link_ALPHA1-3 : bond 0.01303 ( 5) link_ALPHA1-3 : angle 1.60478 ( 15) link_BETA1-4 : bond 0.00446 ( 18) link_BETA1-4 : angle 1.50063 ( 54) link_NAG-ASN : bond 0.00341 ( 48) link_NAG-ASN : angle 2.37972 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 322 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6290 (tp) REVERT: A 359 ILE cc_start: 0.6032 (mm) cc_final: 0.5633 (mt) REVERT: A 377 ASN cc_start: 0.7933 (t0) cc_final: 0.7383 (p0) REVERT: A 456 ARG cc_start: 0.7163 (ttp-170) cc_final: 0.6864 (ptm-80) REVERT: A 491 ILE cc_start: 0.8579 (mt) cc_final: 0.8321 (mm) REVERT: B 575 GLN cc_start: 0.8262 (pp30) cc_final: 0.7849 (pp30) REVERT: C 272 ILE cc_start: 0.7031 (tp) cc_final: 0.6776 (pt) REVERT: C 389 LYS cc_start: 0.8020 (mttt) cc_final: 0.7812 (mtmt) REVERT: C 484 TYR cc_start: 0.7681 (p90) cc_final: 0.7448 (p90) outliers start: 49 outliers final: 38 residues processed: 202 average time/residue: 0.1240 time to fit residues: 39.4561 Evaluate side-chains 188 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 656 ASN Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 540 GLN F 624 ASN A 103 GLN A 302 ASN B 625 ASN H 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.134701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.118975 restraints weight = 39396.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.121677 restraints weight = 23700.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123524 restraints weight = 16449.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.124783 restraints weight = 12588.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.125654 restraints weight = 10339.371| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16871 Z= 0.143 Angle : 0.612 8.017 23041 Z= 0.308 Chirality : 0.045 0.246 2784 Planarity : 0.004 0.036 2804 Dihedral : 5.813 51.905 3556 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.81 % Allowed : 13.41 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.18), residues: 1923 helix: 1.81 (0.25), residues: 428 sheet: 0.25 (0.22), residues: 498 loop : 0.60 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 633 TYR 0.017 0.002 TYR C 435 PHE 0.016 0.002 PHE E 361 TRP 0.020 0.002 TRP C 112 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00329 (16765) covalent geometry : angle 0.58226 (22758) SS BOND : bond 0.00335 ( 35) SS BOND : angle 1.34625 ( 70) hydrogen bonds : bond 0.04200 ( 519) hydrogen bonds : angle 5.17930 ( 1395) link_ALPHA1-3 : bond 0.01168 ( 5) link_ALPHA1-3 : angle 1.51638 ( 15) link_BETA1-4 : bond 0.00454 ( 18) link_BETA1-4 : angle 1.40013 ( 54) link_NAG-ASN : bond 0.00250 ( 48) link_NAG-ASN : angle 2.10306 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 322 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6361 (tp) REVERT: F 518 MET cc_start: 0.6754 (mpp) cc_final: 0.6507 (mpp) REVERT: F 629 MET cc_start: 0.6706 (mmm) cc_final: 0.6366 (mmm) REVERT: A 359 ILE cc_start: 0.5865 (mm) cc_final: 0.5506 (mt) REVERT: A 377 ASN cc_start: 0.7873 (t0) cc_final: 0.7265 (p0) REVERT: A 456 ARG cc_start: 0.7134 (ttp-170) cc_final: 0.6860 (ptm-80) REVERT: A 491 ILE cc_start: 0.8528 (mt) cc_final: 0.8251 (mm) REVERT: B 575 GLN cc_start: 0.8228 (pp30) cc_final: 0.7810 (pp30) REVERT: B 626 MET cc_start: 0.5916 (ttt) cc_final: 0.5634 (ttp) REVERT: C 272 ILE cc_start: 0.7142 (tp) cc_final: 0.6935 (pt) REVERT: C 373 MET cc_start: 0.7954 (ptt) cc_final: 0.7701 (ptt) REVERT: C 389 LYS cc_start: 0.7927 (mttt) cc_final: 0.7401 (ttmt) REVERT: C 484 TYR cc_start: 0.7452 (p90) cc_final: 0.7251 (p90) outliers start: 49 outliers final: 35 residues processed: 202 average time/residue: 0.1257 time to fit residues: 39.5907 Evaluate side-chains 188 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 656 ASN Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 190 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 478 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.135171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.119407 restraints weight = 39663.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.122143 restraints weight = 23896.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.123991 restraints weight = 16554.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.125274 restraints weight = 12669.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.126147 restraints weight = 10373.795| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16871 Z= 0.137 Angle : 0.605 8.771 23041 Z= 0.304 Chirality : 0.045 0.213 2784 Planarity : 0.004 0.036 2804 Dihedral : 5.677 57.604 3556 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.64 % Allowed : 13.58 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 1923 helix: 1.89 (0.25), residues: 422 sheet: 0.21 (0.22), residues: 500 loop : 0.52 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 304 TYR 0.017 0.002 TYR H 33 PHE 0.016 0.002 PHE E 361 TRP 0.018 0.001 TRP C 112 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00312 (16765) covalent geometry : angle 0.57641 (22758) SS BOND : bond 0.00334 ( 35) SS BOND : angle 1.40279 ( 70) hydrogen bonds : bond 0.04043 ( 519) hydrogen bonds : angle 5.08615 ( 1395) link_ALPHA1-3 : bond 0.01164 ( 5) link_ALPHA1-3 : angle 1.55998 ( 15) link_BETA1-4 : bond 0.00455 ( 18) link_BETA1-4 : angle 1.37490 ( 54) link_NAG-ASN : bond 0.00244 ( 48) link_NAG-ASN : angle 2.01575 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 322 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6137 (tp) REVERT: F 518 MET cc_start: 0.6703 (mpp) cc_final: 0.6460 (mpp) REVERT: A 359 ILE cc_start: 0.5986 (mm) cc_final: 0.5571 (mt) REVERT: A 377 ASN cc_start: 0.7838 (t0) cc_final: 0.7231 (p0) REVERT: A 456 ARG cc_start: 0.7146 (ttp-170) cc_final: 0.6875 (ptm-80) REVERT: A 491 ILE cc_start: 0.8508 (mt) cc_final: 0.8233 (mm) REVERT: B 575 GLN cc_start: 0.8236 (pp30) cc_final: 0.7808 (pp30) REVERT: C 272 ILE cc_start: 0.7163 (tp) cc_final: 0.6953 (pt) REVERT: C 300 ASN cc_start: 0.6663 (m-40) cc_final: 0.5897 (t0) REVERT: C 373 MET cc_start: 0.7998 (ptt) cc_final: 0.7713 (ptt) REVERT: C 389 LYS cc_start: 0.7955 (mttt) cc_final: 0.7738 (mtmt) REVERT: H 52 ASN cc_start: 0.6753 (t0) cc_final: 0.6378 (t0) outliers start: 46 outliers final: 34 residues processed: 198 average time/residue: 0.1272 time to fit residues: 39.5597 Evaluate side-chains 187 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 656 ASN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 139 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 229 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.129801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.113775 restraints weight = 39812.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116340 restraints weight = 24551.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.118110 restraints weight = 17420.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119328 restraints weight = 13550.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.120181 restraints weight = 11270.052| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 16871 Z= 0.287 Angle : 0.783 9.700 23041 Z= 0.395 Chirality : 0.051 0.267 2784 Planarity : 0.005 0.045 2804 Dihedral : 6.406 58.668 3556 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.64 % Allowed : 13.24 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 1923 helix: 1.31 (0.25), residues: 424 sheet: -0.20 (0.23), residues: 470 loop : -0.00 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 38 TYR 0.023 0.002 TYR H 33 PHE 0.027 0.003 PHE E 361 TRP 0.023 0.002 TRP H 50 HIS 0.009 0.002 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00682 (16765) covalent geometry : angle 0.75311 (22758) SS BOND : bond 0.00573 ( 35) SS BOND : angle 1.77260 ( 70) hydrogen bonds : bond 0.05046 ( 519) hydrogen bonds : angle 5.66092 ( 1395) link_ALPHA1-3 : bond 0.01004 ( 5) link_ALPHA1-3 : angle 1.63301 ( 15) link_BETA1-4 : bond 0.00428 ( 18) link_BETA1-4 : angle 1.59665 ( 54) link_NAG-ASN : bond 0.00368 ( 48) link_NAG-ASN : angle 2.39439 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 322 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6203 (tp) REVERT: A 359 ILE cc_start: 0.5981 (mm) cc_final: 0.5664 (mt) REVERT: A 377 ASN cc_start: 0.7915 (t0) cc_final: 0.7248 (p0) REVERT: A 456 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.7034 (ptm-80) REVERT: B 575 GLN cc_start: 0.8301 (pp30) cc_final: 0.7900 (pp30) REVERT: C 389 LYS cc_start: 0.8167 (mttt) cc_final: 0.7353 (tptm) REVERT: D 530 MET cc_start: 0.4251 (mtm) cc_final: 0.3144 (mtm) REVERT: D 639 THR cc_start: 0.8060 (m) cc_final: 0.7816 (t) REVERT: H 52 ASN cc_start: 0.6783 (t0) cc_final: 0.6522 (t0) outliers start: 46 outliers final: 38 residues processed: 199 average time/residue: 0.1287 time to fit residues: 39.7158 Evaluate side-chains 190 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 656 ASN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 117 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 344 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN H 52 ASN H 76 ASN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.134848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.119143 restraints weight = 40214.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.121794 restraints weight = 24765.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.123616 restraints weight = 17362.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.124874 restraints weight = 13399.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.125751 restraints weight = 11039.726| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16871 Z= 0.132 Angle : 0.606 8.045 23041 Z= 0.306 Chirality : 0.045 0.184 2784 Planarity : 0.004 0.037 2804 Dihedral : 5.819 55.556 3556 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.78 % Allowed : 14.56 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 1923 helix: 1.62 (0.25), residues: 430 sheet: -0.10 (0.22), residues: 506 loop : 0.17 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 633 TYR 0.015 0.001 TYR C 435 PHE 0.018 0.002 PHE L 62 TRP 0.029 0.002 TRP C 112 HIS 0.006 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00299 (16765) covalent geometry : angle 0.57867 (22758) SS BOND : bond 0.00342 ( 35) SS BOND : angle 1.26032 ( 70) hydrogen bonds : bond 0.04015 ( 519) hydrogen bonds : angle 5.14572 ( 1395) link_ALPHA1-3 : bond 0.01052 ( 5) link_ALPHA1-3 : angle 1.51695 ( 15) link_BETA1-4 : bond 0.00473 ( 18) link_BETA1-4 : angle 1.40506 ( 54) link_NAG-ASN : bond 0.00266 ( 48) link_NAG-ASN : angle 2.01266 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 518 MET cc_start: 0.6657 (mpp) cc_final: 0.6396 (mpp) REVERT: A 359 ILE cc_start: 0.5951 (mm) cc_final: 0.5582 (mt) REVERT: A 377 ASN cc_start: 0.7860 (t0) cc_final: 0.7293 (p0) REVERT: A 456 ARG cc_start: 0.7238 (ttp-170) cc_final: 0.6943 (ptm-80) REVERT: B 529 THR cc_start: 0.6195 (p) cc_final: 0.5910 (p) REVERT: B 530 MET cc_start: 0.6238 (mtt) cc_final: 0.5670 (mtm) REVERT: B 575 GLN cc_start: 0.8252 (pp30) cc_final: 0.7821 (pp30) REVERT: C 272 ILE cc_start: 0.7293 (tp) cc_final: 0.6992 (pt) REVERT: C 373 MET cc_start: 0.8080 (ptt) cc_final: 0.7844 (ptt) REVERT: C 389 LYS cc_start: 0.8050 (mttt) cc_final: 0.7248 (tptm) REVERT: D 530 MET cc_start: 0.4074 (mtm) cc_final: 0.3202 (mtm) outliers start: 31 outliers final: 25 residues processed: 185 average time/residue: 0.1296 time to fit residues: 37.1003 Evaluate side-chains 173 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 656 ASN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 89 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 83 optimal weight: 0.0070 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.135381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.119705 restraints weight = 40002.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.122355 restraints weight = 24679.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.124134 restraints weight = 17338.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.125402 restraints weight = 13410.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.126297 restraints weight = 11042.033| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16871 Z= 0.126 Angle : 0.585 8.384 23041 Z= 0.296 Chirality : 0.044 0.224 2784 Planarity : 0.004 0.037 2804 Dihedral : 5.467 53.626 3556 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.78 % Allowed : 14.79 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1923 helix: 1.89 (0.26), residues: 420 sheet: -0.09 (0.22), residues: 501 loop : 0.22 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 633 TYR 0.012 0.001 TYR E 173 PHE 0.015 0.001 PHE L 62 TRP 0.025 0.002 TRP C 112 HIS 0.007 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00288 (16765) covalent geometry : angle 0.55759 (22758) SS BOND : bond 0.00307 ( 35) SS BOND : angle 1.23800 ( 70) hydrogen bonds : bond 0.03821 ( 519) hydrogen bonds : angle 5.01573 ( 1395) link_ALPHA1-3 : bond 0.00965 ( 5) link_ALPHA1-3 : angle 1.53719 ( 15) link_BETA1-4 : bond 0.00443 ( 18) link_BETA1-4 : angle 1.39462 ( 54) link_NAG-ASN : bond 0.00230 ( 48) link_NAG-ASN : angle 1.95335 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2975.29 seconds wall clock time: 52 minutes 24.43 seconds (3144.43 seconds total)