Starting phenix.real_space_refine on Wed Mar 4 19:13:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l90_23243/03_2026/7l90_23243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l90_23243/03_2026/7l90_23243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l90_23243/03_2026/7l90_23243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l90_23243/03_2026/7l90_23243.map" model { file = "/net/cci-nas-00/data/ceres_data/7l90_23243/03_2026/7l90_23243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l90_23243/03_2026/7l90_23243.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 104 5.16 5 C 9647 2.51 5 N 2630 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15480 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3434 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 4 Chain: "B" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 3439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3439 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 3 Chain: "D" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1018 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "E" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3448 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 20, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 465 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 92} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 93} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "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: 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: "Q" 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: "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: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.12, per 1000 atoms: 0.20 Number of scatterers: 15480 At special positions: 0 Unit cell: (126.69, 123.6, 149.35, 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 104 16.00 O 3099 8.00 N 2630 7.00 C 9647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.07 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.15 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.07 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 332 " " NAG A 604 " - " ASN A 448 " " NAG A 605 " - " ASN A 133 " " NAG A 606 " - " ASN A 137 " " NAG A 607 " - " ASN A 160 " " NAG A 608 " - " ASN A 197 " " NAG A 609 " - " ASN A 234 " " NAG A 610 " - " ASN A 88 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 355 " " NAG A 613 " - " ASN A 241 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 301 " " NAG A 616 " - " ASN A 295 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 160 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG C 613 " - " ASN C 355 " " NAG C 614 " - " ASN C 289 " " NAG C 615 " - " ASN C 88 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 156 " " NAG K 1 " - " ASN B 611 " " NAG M 1 " - " ASN C 386 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN E 386 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 156 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 606.6 milliseconds 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3574 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 32 sheets defined 30.7% alpha, 44.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.111A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.173A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.663A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 624 removed outlier: 4.054A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 624' Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.527A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 3.516A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.193A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 544 removed outlier: 3.528A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 568 through 597 removed outlier: 3.957A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 659 removed outlier: 4.273A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.630A pdb=" N ASN E 98 " --> pdb=" O MET E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 334 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 474 through 481 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 544 through 546 No H-bonds generated for 'chain 'F' and resid 544 through 546' Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'F' and resid 568 through 597 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.575A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 Processing helix chain 'H' and resid 70 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.447A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.086A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.901A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.263A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.512A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.922A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.263A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.512A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.011A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.824A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.464A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB9, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.712A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.917A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.905A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.585A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.675A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.662A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N MET E 426 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.539A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 302 current: chain 'E' and resid 358 through 361 Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.825A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 441 through 456 current: chain 'E' and resid 414 through 421 removed outlier: 4.318A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD4, first strand: chain 'H' and resid 68 through 69 Processing sheet with id=AD5, first strand: chain 'L' and resid 35 through 36 635 hydrogen bonds defined for protein. 1671 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: 2.76 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 3970 1.33 - 1.47: 4762 1.47 - 1.62: 6867 1.62 - 1.76: 23 1.76 - 1.90: 122 Bond restraints: 15744 Sorted by residual: bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.426 -0.100 1.10e-02 8.26e+03 8.28e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.53e+01 bond pdb=" CB ILE C 396 " pdb=" CG1 ILE C 396 " ideal model delta sigma weight residual 1.530 1.665 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CB ILE E 396 " pdb=" CG1 ILE E 396 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 15739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 18222 2.37 - 4.75: 2694 4.75 - 7.12: 445 7.12 - 9.50: 40 9.50 - 11.87: 8 Bond angle restraints: 21409 Sorted by residual: angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.01e+00 9.80e-01 7.88e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.34 -8.78 1.02e+00 9.61e-01 7.40e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 127.80 -8.24 1.02e+00 9.61e-01 6.53e+01 angle pdb=" C LEU C 288 " pdb=" N ASN C 289 " pdb=" CA ASN C 289 " ideal model delta sigma weight residual 120.28 131.10 -10.82 1.34e+00 5.57e-01 6.52e+01 angle pdb=" N ILE B 622 " pdb=" CA ILE B 622 " pdb=" C ILE B 622 " ideal model delta sigma weight residual 110.53 118.01 -7.48 9.40e-01 1.13e+00 6.33e+01 ... (remaining 21404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 10151 21.94 - 43.88: 215 43.88 - 65.83: 78 65.83 - 87.77: 34 87.77 - 109.71: 12 Dihedral angle restraints: 10490 sinusoidal: 5000 harmonic: 5490 Sorted by residual: dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual 93.00 158.92 -65.92 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 158.20 -65.20 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.01 -59.01 1 1.00e+01 1.00e-02 4.66e+01 ... (remaining 10487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1788 0.106 - 0.211: 589 0.211 - 0.317: 183 0.317 - 0.422: 104 0.422 - 0.528: 34 Chirality restraints: 2698 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 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 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 ... (remaining 2695 not shown) Planarity restraints: 2699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 613 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG E 613 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG E 613 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG E 613 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG E 613 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG C 602 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " 0.091 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " -0.524 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.318 2.00e-02 2.50e+03 2.70e-01 9.11e+02 pdb=" C7 NAG K 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " 0.053 2.00e-02 2.50e+03 ... (remaining 2696 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4608 2.84 - 3.36: 14724 3.36 - 3.87: 25490 3.87 - 4.39: 29810 4.39 - 4.90: 46333 Nonbonded interactions: 120965 Sorted by model distance: nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.330 3.040 nonbonded pdb=" NH1 ARG E 503 " pdb=" OE1 GLN F 650 " model vdw 2.428 3.120 nonbonded pdb=" N UNK L 51 " pdb=" N UNK L 52 " model vdw 2.477 2.560 nonbonded pdb=" O UNK L 32 " pdb=" N UNK L 49 " model vdw 2.482 3.120 nonbonded pdb=" NZ LYS C 97 " pdb=" OE2 GLU C 275 " model vdw 2.484 3.120 ... (remaining 120960 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 33 through 57 or resid 66 through 615)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 141 or resid 152 through \ 615)) selection = (chain 'E' and (resid 33 through 141 or resid 152 through 615)) } ncs_group { reference = (chain 'B' and (resid 521 through 661 or resid 701 through 702)) selection = chain 'D' selection = (chain 'F' and (resid 521 through 661 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 17 through 109) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.800 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.022 0.159 15855 Z= 1.153 Angle : 1.793 13.832 21709 Z= 1.140 Chirality : 0.141 0.528 2698 Planarity : 0.016 0.302 2637 Dihedral : 11.858 109.709 6817 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1656 helix: -0.03 (0.23), residues: 418 sheet: 1.00 (0.24), residues: 413 loop : 0.68 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 273 TYR 0.065 0.008 TYR A 191 PHE 0.032 0.006 PHE C 383 TRP 0.067 0.008 TRP F 571 HIS 0.010 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.02092 (15744) covalent geometry : angle 1.76273 (21409) SS BOND : bond 0.02683 ( 33) SS BOND : angle 3.07185 ( 66) hydrogen bonds : bond 0.17940 ( 557) hydrogen bonds : angle 7.57642 ( 1671) link_ALPHA1-3 : bond 0.08121 ( 3) link_ALPHA1-3 : angle 5.65982 ( 9) link_BETA1-4 : bond 0.07231 ( 13) link_BETA1-4 : angle 4.84911 ( 39) link_NAG-ASN : bond 0.07717 ( 62) link_NAG-ASN : angle 2.76563 ( 186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.564 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8501 (m100) cc_final: 0.8016 (m100) REVERT: A 50 THR cc_start: 0.8861 (t) cc_final: 0.8493 (t) REVERT: A 120 VAL cc_start: 0.9231 (t) cc_final: 0.8278 (t) REVERT: A 356 ASN cc_start: 0.7920 (t0) cc_final: 0.7567 (p0) REVERT: B 523 LEU cc_start: 0.8675 (mt) cc_final: 0.8274 (mt) REVERT: B 566 LEU cc_start: 0.8753 (mt) cc_final: 0.8527 (pp) REVERT: B 650 GLN cc_start: 0.8938 (tp40) cc_final: 0.8517 (tm-30) REVERT: C 46 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8736 (mmmt) REVERT: C 50 THR cc_start: 0.9398 (t) cc_final: 0.9137 (t) REVERT: C 80 ASN cc_start: 0.8765 (m-40) cc_final: 0.8408 (t0) REVERT: C 168 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8520 (mtmt) REVERT: C 190 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8595 (mp0) REVERT: C 316 TRP cc_start: 0.8541 (m100) cc_final: 0.7840 (m100) REVERT: C 338 TRP cc_start: 0.9582 (t-100) cc_final: 0.9184 (t-100) REVERT: C 349 LEU cc_start: 0.9692 (mt) cc_final: 0.9472 (mt) REVERT: C 390 LEU cc_start: 0.9458 (tp) cc_final: 0.8734 (tp) REVERT: C 391 PHE cc_start: 0.8838 (m-80) cc_final: 0.8370 (m-10) REVERT: C 475 MET cc_start: 0.8871 (mmt) cc_final: 0.8646 (mmm) REVERT: D 537 LEU cc_start: 0.9366 (mt) cc_final: 0.9015 (mt) REVERT: D 538 THR cc_start: 0.9411 (p) cc_final: 0.9161 (t) REVERT: D 539 VAL cc_start: 0.9258 (t) cc_final: 0.8836 (t) REVERT: D 543 ASN cc_start: 0.8558 (m-40) cc_final: 0.8352 (m-40) REVERT: D 586 TYR cc_start: 0.9356 (t80) cc_final: 0.8729 (t80) REVERT: D 588 ARG cc_start: 0.8923 (ttp-170) cc_final: 0.8626 (ttp80) REVERT: D 596 TRP cc_start: 0.8849 (m-10) cc_final: 0.8200 (m-10) REVERT: D 607 ASN cc_start: 0.8852 (m-40) cc_final: 0.8253 (m-40) REVERT: E 72 HIS cc_start: 0.8933 (m-70) cc_final: 0.8641 (m-70) REVERT: E 95 MET cc_start: 0.9116 (ptt) cc_final: 0.8317 (ptm) REVERT: E 141 ASP cc_start: 0.9025 (m-30) cc_final: 0.8820 (p0) REVERT: E 180 ASP cc_start: 0.8343 (m-30) cc_final: 0.7801 (m-30) REVERT: E 381 GLU cc_start: 0.8924 (tp30) cc_final: 0.8446 (tp30) REVERT: E 423 ILE cc_start: 0.9669 (mt) cc_final: 0.9339 (mm) REVERT: E 452 LEU cc_start: 0.9261 (mp) cc_final: 0.8526 (mp) REVERT: E 489 VAL cc_start: 0.9106 (m) cc_final: 0.8901 (m) REVERT: E 490 LYS cc_start: 0.9430 (pttt) cc_final: 0.9098 (tptt) REVERT: E 491 ILE cc_start: 0.9391 (mm) cc_final: 0.9150 (mm) REVERT: F 567 LYS cc_start: 0.9200 (mttt) cc_final: 0.8949 (mmtm) REVERT: F 592 LEU cc_start: 0.9280 (mt) cc_final: 0.8931 (mt) REVERT: F 596 TRP cc_start: 0.8552 (m-10) cc_final: 0.8021 (m-10) REVERT: F 607 ASN cc_start: 0.8813 (m-40) cc_final: 0.8473 (p0) REVERT: F 650 GLN cc_start: 0.9000 (tp40) cc_final: 0.8320 (tm-30) REVERT: F 661 LEU cc_start: 0.8280 (tp) cc_final: 0.7608 (tp) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.1198 time to fit residues: 91.5806 Evaluate side-chains 265 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 630 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS D 630 GLN D 653 GLN E 130 GLN E 352 HIS E 432 GLN F 591 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060337 restraints weight = 72034.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062241 restraints weight = 39421.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063561 restraints weight = 25638.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064349 restraints weight = 18707.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065086 restraints weight = 15149.858| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15855 Z= 0.180 Angle : 0.884 19.641 21709 Z= 0.425 Chirality : 0.051 0.335 2698 Planarity : 0.005 0.090 2637 Dihedral : 8.580 74.495 3616 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.33 % Allowed : 2.65 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1656 helix: 0.83 (0.25), residues: 412 sheet: 0.85 (0.24), residues: 435 loop : 0.34 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 166 TYR 0.027 0.002 TYR F 643 PHE 0.016 0.002 PHE A 353 TRP 0.033 0.003 TRP A 69 HIS 0.008 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00377 (15744) covalent geometry : angle 0.79915 (21409) SS BOND : bond 0.00579 ( 33) SS BOND : angle 1.45447 ( 66) hydrogen bonds : bond 0.06646 ( 557) hydrogen bonds : angle 5.73954 ( 1671) link_ALPHA1-3 : bond 0.01416 ( 3) link_ALPHA1-3 : angle 3.14626 ( 9) link_BETA1-4 : bond 0.00897 ( 13) link_BETA1-4 : angle 3.03151 ( 39) link_NAG-ASN : bond 0.00697 ( 62) link_NAG-ASN : angle 3.81830 ( 186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 372 time to evaluate : 0.333 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8724 (m100) cc_final: 0.8034 (m100) REVERT: A 98 ASN cc_start: 0.8349 (t0) cc_final: 0.8145 (t0) REVERT: A 104 MET cc_start: 0.9140 (tpp) cc_final: 0.8925 (mmm) REVERT: A 109 ILE cc_start: 0.9543 (tt) cc_final: 0.9196 (pt) REVERT: A 114 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8780 (tm-30) REVERT: A 123 THR cc_start: 0.9556 (m) cc_final: 0.9315 (m) REVERT: A 288 LEU cc_start: 0.9566 (mp) cc_final: 0.9293 (mp) REVERT: A 356 ASN cc_start: 0.7604 (t0) cc_final: 0.7146 (p0) REVERT: A 452 LEU cc_start: 0.9501 (mt) cc_final: 0.9094 (mt) REVERT: B 595 ILE cc_start: 0.9522 (tt) cc_final: 0.9319 (tp) REVERT: B 602 LEU cc_start: 0.8966 (mt) cc_final: 0.8630 (pt) REVERT: B 603 ILE cc_start: 0.8733 (mt) cc_final: 0.8447 (tp) REVERT: B 634 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 635 ILE cc_start: 0.9537 (tp) cc_final: 0.9288 (tp) REVERT: B 650 GLN cc_start: 0.8879 (tp40) cc_final: 0.8407 (tm-30) REVERT: B 654 GLU cc_start: 0.9221 (tp30) cc_final: 0.8851 (tp30) REVERT: C 46 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8527 (mmmt) REVERT: C 95 MET cc_start: 0.9226 (ptt) cc_final: 0.8793 (ptt) REVERT: C 98 ASN cc_start: 0.8942 (t0) cc_final: 0.8469 (t0) REVERT: C 100 MET cc_start: 0.9171 (mtm) cc_final: 0.8754 (mtm) REVERT: C 116 LEU cc_start: 0.9550 (pp) cc_final: 0.9339 (tp) REVERT: C 168 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8363 (mtmt) REVERT: C 259 LEU cc_start: 0.9115 (mm) cc_final: 0.8910 (mm) REVERT: C 316 TRP cc_start: 0.8450 (m100) cc_final: 0.7819 (m100) REVERT: C 338 TRP cc_start: 0.9539 (t-100) cc_final: 0.9219 (t-100) REVERT: C 374 HIS cc_start: 0.9026 (t70) cc_final: 0.8794 (t70) REVERT: C 390 LEU cc_start: 0.9407 (tp) cc_final: 0.8702 (tp) REVERT: C 391 PHE cc_start: 0.8931 (m-80) cc_final: 0.8309 (m-10) REVERT: C 477 ASP cc_start: 0.9556 (m-30) cc_final: 0.9090 (m-30) REVERT: D 522 PHE cc_start: 0.8238 (t80) cc_final: 0.7492 (t80) REVERT: D 536 THR cc_start: 0.9342 (p) cc_final: 0.9129 (p) REVERT: D 538 THR cc_start: 0.9429 (p) cc_final: 0.9120 (t) REVERT: D 579 ARG cc_start: 0.8356 (mtt180) cc_final: 0.7634 (mtp180) REVERT: D 586 TYR cc_start: 0.9248 (t80) cc_final: 0.8913 (t80) REVERT: D 588 ARG cc_start: 0.8914 (ttp-170) cc_final: 0.8247 (tmm-80) REVERT: D 589 ASP cc_start: 0.9249 (m-30) cc_final: 0.8977 (m-30) REVERT: D 595 ILE cc_start: 0.9672 (mm) cc_final: 0.9305 (tp) REVERT: D 596 TRP cc_start: 0.8370 (m-10) cc_final: 0.7933 (m-90) REVERT: D 603 ILE cc_start: 0.9141 (tt) cc_final: 0.8815 (mm) REVERT: D 607 ASN cc_start: 0.8663 (m-40) cc_final: 0.8119 (p0) REVERT: D 628 TRP cc_start: 0.7527 (t-100) cc_final: 0.6817 (t-100) REVERT: D 631 TRP cc_start: 0.8536 (t-100) cc_final: 0.8278 (t-100) REVERT: E 39 TYR cc_start: 0.8812 (m-80) cc_final: 0.8585 (m-80) REVERT: E 72 HIS cc_start: 0.8827 (m-70) cc_final: 0.8333 (m-70) REVERT: E 97 LYS cc_start: 0.9367 (mtpp) cc_final: 0.9123 (mtpp) REVERT: E 104 MET cc_start: 0.9333 (ttm) cc_final: 0.9108 (ttp) REVERT: E 141 ASP cc_start: 0.8934 (m-30) cc_final: 0.8682 (p0) REVERT: E 180 ASP cc_start: 0.8425 (m-30) cc_final: 0.7925 (m-30) REVERT: E 489 VAL cc_start: 0.9054 (m) cc_final: 0.8600 (m) REVERT: F 567 LYS cc_start: 0.9297 (mttt) cc_final: 0.8914 (mmtm) REVERT: F 577 GLN cc_start: 0.9346 (tt0) cc_final: 0.8975 (tp40) REVERT: F 601 LYS cc_start: 0.9035 (mmpt) cc_final: 0.8395 (mtpp) REVERT: F 602 LEU cc_start: 0.9594 (mt) cc_final: 0.9147 (mt) REVERT: F 633 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8608 (mttm) REVERT: F 650 GLN cc_start: 0.8872 (tp40) cc_final: 0.8390 (tm-30) outliers start: 5 outliers final: 1 residues processed: 377 average time/residue: 0.1195 time to fit residues: 65.8022 Evaluate side-chains 258 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 2 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 591 GLN B 658 GLN C 249 HIS C 302 ASN C 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN F 564 HIS F 658 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056671 restraints weight = 75008.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058240 restraints weight = 44645.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.059323 restraints weight = 30922.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060122 restraints weight = 23651.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060556 restraints weight = 19372.268| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 15855 Z= 0.245 Angle : 0.827 16.929 21709 Z= 0.404 Chirality : 0.048 0.361 2698 Planarity : 0.004 0.074 2637 Dihedral : 7.485 56.550 3616 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.13 % Allowed : 3.25 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1656 helix: 0.51 (0.26), residues: 421 sheet: 0.70 (0.24), residues: 433 loop : 0.09 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 166 TYR 0.023 0.002 TYR D 643 PHE 0.016 0.002 PHE D 522 TRP 0.038 0.003 TRP A 427 HIS 0.009 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00533 (15744) covalent geometry : angle 0.76900 (21409) SS BOND : bond 0.00329 ( 33) SS BOND : angle 1.48138 ( 66) hydrogen bonds : bond 0.05693 ( 557) hydrogen bonds : angle 5.41968 ( 1671) link_ALPHA1-3 : bond 0.00712 ( 3) link_ALPHA1-3 : angle 2.74307 ( 9) link_BETA1-4 : bond 0.00424 ( 13) link_BETA1-4 : angle 2.50084 ( 39) link_NAG-ASN : bond 0.00474 ( 62) link_NAG-ASN : angle 3.05236 ( 186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 0.471 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: symmetry clash 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: A 104 MET cc_start: 0.9000 (tpp) cc_final: 0.8640 (mmm) REVERT: A 114 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8868 (tm-30) REVERT: A 288 LEU cc_start: 0.9546 (mp) cc_final: 0.9284 (mp) REVERT: A 356 ASN cc_start: 0.7486 (t0) cc_final: 0.6953 (p0) REVERT: B 630 GLN cc_start: 0.8840 (mp10) cc_final: 0.8536 (mp10) REVERT: B 634 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 635 ILE cc_start: 0.9544 (tp) cc_final: 0.9209 (tp) REVERT: B 650 GLN cc_start: 0.8898 (tp40) cc_final: 0.8495 (tm-30) REVERT: C 46 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8534 (mmmt) REVERT: C 95 MET cc_start: 0.9121 (ptt) cc_final: 0.8685 (ptt) REVERT: C 168 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8593 (mtmt) REVERT: C 316 TRP cc_start: 0.8605 (m100) cc_final: 0.8318 (m100) REVERT: C 338 TRP cc_start: 0.9479 (t-100) cc_final: 0.9164 (t-100) REVERT: C 390 LEU cc_start: 0.9395 (tp) cc_final: 0.8947 (tp) REVERT: C 449 ILE cc_start: 0.8987 (mt) cc_final: 0.8748 (tt) REVERT: C 475 MET cc_start: 0.8337 (mmm) cc_final: 0.6963 (mmm) REVERT: C 477 ASP cc_start: 0.9375 (m-30) cc_final: 0.8876 (m-30) REVERT: C 479 TRP cc_start: 0.8726 (m-10) cc_final: 0.8402 (m-90) REVERT: D 579 ARG cc_start: 0.8357 (mtt180) cc_final: 0.7784 (mtp180) REVERT: D 585 ARG cc_start: 0.8920 (mtp-110) cc_final: 0.8359 (ptm160) REVERT: D 588 ARG cc_start: 0.8931 (ttp-170) cc_final: 0.8121 (tmm-80) REVERT: D 595 ILE cc_start: 0.9672 (mm) cc_final: 0.9466 (tp) REVERT: D 596 TRP cc_start: 0.8556 (m-10) cc_final: 0.8168 (m-90) REVERT: E 33 ASN cc_start: 0.8550 (t0) cc_final: 0.8312 (t0) REVERT: E 97 LYS cc_start: 0.9424 (mtpp) cc_final: 0.9163 (mtpp) REVERT: E 180 ASP cc_start: 0.8489 (m-30) cc_final: 0.8168 (m-30) REVERT: F 567 LYS cc_start: 0.9336 (mttt) cc_final: 0.8998 (mmtm) REVERT: F 592 LEU cc_start: 0.9401 (tp) cc_final: 0.9025 (tp) REVERT: F 595 ILE cc_start: 0.9822 (mm) cc_final: 0.9262 (tt) REVERT: F 596 TRP cc_start: 0.8568 (m-10) cc_final: 0.7590 (m-10) REVERT: F 602 LEU cc_start: 0.9561 (mt) cc_final: 0.9158 (mt) REVERT: F 643 TYR cc_start: 0.9315 (m-10) cc_final: 0.9098 (m-80) REVERT: F 661 LEU cc_start: 0.8259 (tp) cc_final: 0.7844 (tt) outliers start: 2 outliers final: 1 residues processed: 314 average time/residue: 0.1156 time to fit residues: 53.6697 Evaluate side-chains 227 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS C 103 GLN C 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN F 591 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.067560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055631 restraints weight = 76197.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.057216 restraints weight = 45049.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058301 restraints weight = 30853.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.059114 restraints weight = 23389.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.059547 restraints weight = 18951.545| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15855 Z= 0.216 Angle : 0.763 14.091 21709 Z= 0.372 Chirality : 0.047 0.314 2698 Planarity : 0.004 0.070 2637 Dihedral : 6.788 59.988 3616 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1656 helix: 0.51 (0.26), residues: 415 sheet: 0.34 (0.24), residues: 440 loop : -0.15 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 588 TYR 0.025 0.002 TYR D 643 PHE 0.022 0.002 PHE E 376 TRP 0.042 0.003 TRP A 427 HIS 0.010 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00473 (15744) covalent geometry : angle 0.70969 (21409) SS BOND : bond 0.00600 ( 33) SS BOND : angle 1.23335 ( 66) hydrogen bonds : bond 0.05034 ( 557) hydrogen bonds : angle 5.24607 ( 1671) link_ALPHA1-3 : bond 0.00656 ( 3) link_ALPHA1-3 : angle 2.83572 ( 9) link_BETA1-4 : bond 0.00224 ( 13) link_BETA1-4 : angle 2.19464 ( 39) link_NAG-ASN : bond 0.00494 ( 62) link_NAG-ASN : angle 2.82089 ( 186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 282 time to evaluate : 0.520 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: symmetry clash 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: A 104 MET cc_start: 0.8963 (tpp) cc_final: 0.8661 (tmm) REVERT: A 288 LEU cc_start: 0.9517 (mp) cc_final: 0.9238 (mp) REVERT: A 475 MET cc_start: 0.8827 (mmm) cc_final: 0.6959 (mmm) REVERT: B 634 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 635 ILE cc_start: 0.9566 (tp) cc_final: 0.9117 (tp) REVERT: B 657 GLU cc_start: 0.8903 (tp30) cc_final: 0.8311 (tp30) REVERT: C 46 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8442 (mmmt) REVERT: C 95 MET cc_start: 0.9017 (ptt) cc_final: 0.8633 (ptt) REVERT: C 168 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8709 (mtmm) REVERT: C 316 TRP cc_start: 0.8696 (m100) cc_final: 0.8315 (m100) REVERT: C 338 TRP cc_start: 0.9472 (t-100) cc_final: 0.9096 (t-100) REVERT: C 390 LEU cc_start: 0.9384 (tp) cc_final: 0.8993 (tp) REVERT: C 424 ILE cc_start: 0.9378 (pt) cc_final: 0.9162 (pt) REVERT: C 426 MET cc_start: 0.9051 (tpt) cc_final: 0.8560 (tpp) REVERT: C 449 ILE cc_start: 0.9112 (mt) cc_final: 0.8904 (tt) REVERT: C 475 MET cc_start: 0.8349 (mmm) cc_final: 0.7397 (mmm) REVERT: C 477 ASP cc_start: 0.9344 (m-30) cc_final: 0.9140 (m-30) REVERT: D 579 ARG cc_start: 0.8374 (mtt180) cc_final: 0.7885 (mtp180) REVERT: D 585 ARG cc_start: 0.8991 (mtp-110) cc_final: 0.8717 (mtp-110) REVERT: D 588 ARG cc_start: 0.8901 (ttp-170) cc_final: 0.8202 (tmm-80) REVERT: D 589 ASP cc_start: 0.9276 (m-30) cc_final: 0.9052 (m-30) REVERT: D 595 ILE cc_start: 0.9704 (mm) cc_final: 0.9362 (tp) REVERT: D 596 TRP cc_start: 0.8523 (m-10) cc_final: 0.8153 (m-90) REVERT: E 95 MET cc_start: 0.9088 (ppp) cc_final: 0.8395 (ppp) REVERT: E 97 LYS cc_start: 0.9393 (mtpp) cc_final: 0.9012 (mtpp) REVERT: E 161 MET cc_start: 0.9034 (tpp) cc_final: 0.8800 (tpt) REVERT: E 180 ASP cc_start: 0.8669 (m-30) cc_final: 0.8235 (m-30) REVERT: F 567 LYS cc_start: 0.9434 (mttt) cc_final: 0.9050 (mmtm) REVERT: F 595 ILE cc_start: 0.9748 (mm) cc_final: 0.9332 (tt) REVERT: F 596 TRP cc_start: 0.8486 (m-10) cc_final: 0.7700 (m-90) REVERT: F 643 TYR cc_start: 0.9340 (m-10) cc_final: 0.8962 (m-80) REVERT: F 646 LEU cc_start: 0.9504 (mt) cc_final: 0.9300 (mt) REVERT: F 653 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8652 (tm-30) REVERT: F 661 LEU cc_start: 0.8218 (tp) cc_final: 0.7996 (tt) outliers start: 2 outliers final: 0 residues processed: 283 average time/residue: 0.1193 time to fit residues: 49.9457 Evaluate side-chains 211 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 182 optimal weight: 40.0000 chunk 85 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 181 optimal weight: 40.0000 chunk 129 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN F 591 GLN F 658 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.054583 restraints weight = 77578.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056303 restraints weight = 43436.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057495 restraints weight = 28887.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.058216 restraints weight = 21469.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058852 restraints weight = 17648.752| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15855 Z= 0.233 Angle : 0.772 11.071 21709 Z= 0.375 Chirality : 0.047 0.327 2698 Planarity : 0.004 0.059 2637 Dihedral : 7.030 58.151 3616 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.13 % Allowed : 2.12 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1656 helix: 0.31 (0.26), residues: 422 sheet: 0.17 (0.24), residues: 424 loop : -0.27 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 617 TYR 0.031 0.002 TYR D 643 PHE 0.018 0.002 PHE E 391 TRP 0.047 0.002 TRP D 614 HIS 0.009 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00508 (15744) covalent geometry : angle 0.71762 (21409) SS BOND : bond 0.00418 ( 33) SS BOND : angle 1.20034 ( 66) hydrogen bonds : bond 0.05032 ( 557) hydrogen bonds : angle 5.20342 ( 1671) link_ALPHA1-3 : bond 0.00651 ( 3) link_ALPHA1-3 : angle 2.79967 ( 9) link_BETA1-4 : bond 0.00253 ( 13) link_BETA1-4 : angle 2.16638 ( 39) link_NAG-ASN : bond 0.00522 ( 62) link_NAG-ASN : angle 2.89854 ( 186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.529 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8741 (m-30) cc_final: 0.8271 (m-30) REVERT: A 475 MET cc_start: 0.8781 (mmm) cc_final: 0.7643 (mmm) REVERT: A 490 LYS cc_start: 0.9136 (ttpt) cc_final: 0.8833 (ttpp) REVERT: B 601 LYS cc_start: 0.9199 (pttm) cc_final: 0.8839 (pttm) REVERT: B 634 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7895 (tm-30) REVERT: B 635 ILE cc_start: 0.9567 (tp) cc_final: 0.9121 (tp) REVERT: B 638 TYR cc_start: 0.8563 (m-80) cc_final: 0.8270 (m-10) REVERT: B 654 GLU cc_start: 0.9348 (tp30) cc_final: 0.8991 (tp30) REVERT: B 657 GLU cc_start: 0.8964 (tp30) cc_final: 0.8325 (tp30) REVERT: C 46 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8370 (mmmt) REVERT: C 49 GLU cc_start: 0.8403 (tp30) cc_final: 0.8109 (tp30) REVERT: C 98 ASN cc_start: 0.9242 (t0) cc_final: 0.8662 (t0) REVERT: C 125 LEU cc_start: 0.9509 (tp) cc_final: 0.9207 (tt) REVERT: C 168 LYS cc_start: 0.9252 (mmtt) cc_final: 0.8880 (mtpt) REVERT: C 316 TRP cc_start: 0.8689 (m100) cc_final: 0.8355 (m100) REVERT: C 338 TRP cc_start: 0.9493 (t-100) cc_final: 0.9118 (t-100) REVERT: C 390 LEU cc_start: 0.9379 (tp) cc_final: 0.8944 (tp) REVERT: C 424 ILE cc_start: 0.9434 (pt) cc_final: 0.9138 (pt) REVERT: C 449 ILE cc_start: 0.9190 (mt) cc_final: 0.8974 (tt) REVERT: D 542 ARG cc_start: 0.8750 (ttp-110) cc_final: 0.8393 (ttp-110) REVERT: D 579 ARG cc_start: 0.8411 (mtt180) cc_final: 0.7953 (mtp180) REVERT: D 588 ARG cc_start: 0.8940 (ttp-170) cc_final: 0.8271 (tmm-80) REVERT: E 72 HIS cc_start: 0.8823 (m-70) cc_final: 0.7906 (m-70) REVERT: E 95 MET cc_start: 0.9233 (ppp) cc_final: 0.8553 (ppp) REVERT: E 97 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9060 (mtpp) REVERT: E 180 ASP cc_start: 0.8664 (m-30) cc_final: 0.8328 (m-30) REVERT: E 381 GLU cc_start: 0.8673 (tp30) cc_final: 0.8385 (tt0) REVERT: F 567 LYS cc_start: 0.9435 (mttt) cc_final: 0.9008 (mmtm) REVERT: F 585 ARG cc_start: 0.9096 (mmt180) cc_final: 0.8740 (ttm-80) REVERT: F 596 TRP cc_start: 0.8465 (m-10) cc_final: 0.8057 (m-10) REVERT: F 601 LYS cc_start: 0.9323 (mmpt) cc_final: 0.8700 (ttmt) REVERT: F 635 ILE cc_start: 0.8934 (pt) cc_final: 0.7791 (pt) REVERT: F 643 TYR cc_start: 0.9322 (m-10) cc_final: 0.9120 (m-80) outliers start: 2 outliers final: 1 residues processed: 277 average time/residue: 0.1241 time to fit residues: 50.8014 Evaluate side-chains 202 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 182 optimal weight: 40.0000 chunk 58 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055259 restraints weight = 77351.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056825 restraints weight = 45610.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057917 restraints weight = 31265.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.058660 restraints weight = 23716.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.059259 restraints weight = 19398.878| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15855 Z= 0.192 Angle : 0.747 12.191 21709 Z= 0.359 Chirality : 0.046 0.318 2698 Planarity : 0.004 0.054 2637 Dihedral : 6.955 58.180 3616 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.07 % Allowed : 1.86 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1656 helix: 0.41 (0.26), residues: 415 sheet: 0.11 (0.24), residues: 423 loop : -0.31 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 588 TYR 0.024 0.002 TYR D 643 PHE 0.023 0.002 PHE E 376 TRP 0.062 0.003 TRP D 596 HIS 0.011 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00424 (15744) covalent geometry : angle 0.68597 (21409) SS BOND : bond 0.00384 ( 33) SS BOND : angle 1.25767 ( 66) hydrogen bonds : bond 0.04750 ( 557) hydrogen bonds : angle 5.11542 ( 1671) link_ALPHA1-3 : bond 0.00644 ( 3) link_ALPHA1-3 : angle 2.64491 ( 9) link_BETA1-4 : bond 0.00248 ( 13) link_BETA1-4 : angle 2.02913 ( 39) link_NAG-ASN : bond 0.00490 ( 62) link_NAG-ASN : angle 3.04685 ( 186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.510 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7857 (m-80) cc_final: 0.7551 (m-80) REVERT: A 180 ASP cc_start: 0.8665 (m-30) cc_final: 0.8355 (m-30) REVERT: A 288 LEU cc_start: 0.9426 (mp) cc_final: 0.9197 (mp) REVERT: A 475 MET cc_start: 0.8766 (mmm) cc_final: 0.8043 (mmm) REVERT: A 490 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8582 (ttpp) REVERT: B 601 LYS cc_start: 0.9240 (pttm) cc_final: 0.8879 (pttm) REVERT: B 630 GLN cc_start: 0.8905 (mp10) cc_final: 0.8642 (mp10) REVERT: B 634 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 635 ILE cc_start: 0.9563 (tp) cc_final: 0.9103 (tp) REVERT: B 638 TYR cc_start: 0.8468 (m-80) cc_final: 0.8093 (m-10) REVERT: B 650 GLN cc_start: 0.8915 (tp40) cc_final: 0.8519 (tm-30) REVERT: B 657 GLU cc_start: 0.8892 (tp30) cc_final: 0.8294 (tp30) REVERT: C 49 GLU cc_start: 0.8440 (tp30) cc_final: 0.8061 (tp30) REVERT: C 80 ASN cc_start: 0.9033 (t0) cc_final: 0.8778 (t0) REVERT: C 95 MET cc_start: 0.9219 (ptm) cc_final: 0.7992 (ppp) REVERT: C 98 ASN cc_start: 0.9269 (t0) cc_final: 0.8805 (t0) REVERT: C 168 LYS cc_start: 0.9290 (mmtt) cc_final: 0.8929 (mtpt) REVERT: C 271 ILE cc_start: 0.8723 (mt) cc_final: 0.8383 (mt) REVERT: C 316 TRP cc_start: 0.8662 (m100) cc_final: 0.8292 (m100) REVERT: C 338 TRP cc_start: 0.9457 (t-100) cc_final: 0.9055 (t-100) REVERT: C 390 LEU cc_start: 0.9390 (tp) cc_final: 0.8963 (tp) REVERT: C 424 ILE cc_start: 0.9351 (pt) cc_final: 0.9141 (pt) REVERT: C 426 MET cc_start: 0.9134 (tpt) cc_final: 0.8765 (tpp) REVERT: C 502 LYS cc_start: 0.9094 (tttp) cc_final: 0.8799 (tptp) REVERT: D 522 PHE cc_start: 0.9022 (t80) cc_final: 0.8655 (t80) REVERT: D 542 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8319 (ttp-110) REVERT: D 579 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7988 (mtp180) REVERT: D 585 ARG cc_start: 0.9065 (mtp-110) cc_final: 0.8496 (mmm-85) REVERT: D 631 TRP cc_start: 0.8691 (t-100) cc_final: 0.8245 (t-100) REVERT: E 33 ASN cc_start: 0.8674 (t0) cc_final: 0.8419 (t0) REVERT: E 72 HIS cc_start: 0.8492 (m-70) cc_final: 0.8055 (m-70) REVERT: E 95 MET cc_start: 0.9199 (ppp) cc_final: 0.8517 (ppp) REVERT: E 97 LYS cc_start: 0.9385 (mtpp) cc_final: 0.9022 (mtpp) REVERT: E 100 MET cc_start: 0.9618 (mtt) cc_final: 0.9333 (mtt) REVERT: E 180 ASP cc_start: 0.8592 (m-30) cc_final: 0.8130 (m-30) REVERT: E 381 GLU cc_start: 0.8655 (tp30) cc_final: 0.8372 (tt0) REVERT: F 567 LYS cc_start: 0.9396 (mttt) cc_final: 0.8978 (mmtm) REVERT: F 596 TRP cc_start: 0.8344 (m-10) cc_final: 0.7972 (m-90) REVERT: F 601 LYS cc_start: 0.9162 (mmpt) cc_final: 0.8923 (mmmt) REVERT: F 635 ILE cc_start: 0.8903 (pt) cc_final: 0.7747 (pt) REVERT: F 643 TYR cc_start: 0.9345 (m-10) cc_final: 0.9134 (m-80) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.1225 time to fit residues: 49.5975 Evaluate side-chains 208 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 139 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 203 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN F 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.068397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056561 restraints weight = 75359.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058155 restraints weight = 44027.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.059244 restraints weight = 29918.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059871 restraints weight = 22654.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060514 restraints weight = 18696.841| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.141 15855 Z= 0.138 Angle : 0.716 18.243 21709 Z= 0.343 Chirality : 0.046 0.293 2698 Planarity : 0.004 0.054 2637 Dihedral : 6.428 56.692 3616 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.13 % Allowed : 1.19 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1656 helix: 0.45 (0.26), residues: 414 sheet: -0.02 (0.24), residues: 423 loop : -0.29 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 588 TYR 0.025 0.002 TYR D 643 PHE 0.014 0.001 PHE E 391 TRP 0.068 0.002 TRP D 596 HIS 0.008 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00313 (15744) covalent geometry : angle 0.65740 (21409) SS BOND : bond 0.00406 ( 33) SS BOND : angle 1.80349 ( 66) hydrogen bonds : bond 0.04438 ( 557) hydrogen bonds : angle 4.95719 ( 1671) link_ALPHA1-3 : bond 0.00839 ( 3) link_ALPHA1-3 : angle 2.41682 ( 9) link_BETA1-4 : bond 0.00322 ( 13) link_BETA1-4 : angle 1.86669 ( 39) link_NAG-ASN : bond 0.00468 ( 62) link_NAG-ASN : angle 2.81538 ( 186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 280 time to evaluate : 0.528 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8582 (m-30) cc_final: 0.8342 (m-30) REVERT: A 288 LEU cc_start: 0.9406 (mp) cc_final: 0.9133 (mp) REVERT: A 475 MET cc_start: 0.8707 (mmm) cc_final: 0.8172 (mmm) REVERT: B 601 LYS cc_start: 0.9297 (pttm) cc_final: 0.8944 (pttm) REVERT: B 634 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7731 (tm-30) REVERT: B 635 ILE cc_start: 0.9539 (tp) cc_final: 0.9037 (tp) REVERT: B 638 TYR cc_start: 0.8527 (m-80) cc_final: 0.8121 (m-10) REVERT: B 657 GLU cc_start: 0.8868 (tp30) cc_final: 0.8203 (tp30) REVERT: C 46 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8568 (tttm) REVERT: C 49 GLU cc_start: 0.8470 (tp30) cc_final: 0.8059 (tp30) REVERT: C 80 ASN cc_start: 0.9047 (t0) cc_final: 0.8799 (t0) REVERT: C 95 MET cc_start: 0.9182 (ptm) cc_final: 0.7951 (ppp) REVERT: C 100 MET cc_start: 0.9381 (mtm) cc_final: 0.8835 (mpp) REVERT: C 104 MET cc_start: 0.9004 (ptm) cc_final: 0.8790 (ppp) REVERT: C 125 LEU cc_start: 0.9494 (tp) cc_final: 0.9201 (tt) REVERT: C 168 LYS cc_start: 0.9293 (mmtt) cc_final: 0.8891 (mtpt) REVERT: C 203 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8922 (pp30) REVERT: C 271 ILE cc_start: 0.8592 (mt) cc_final: 0.8245 (mt) REVERT: C 316 TRP cc_start: 0.8615 (m100) cc_final: 0.8157 (m100) REVERT: C 338 TRP cc_start: 0.9441 (t-100) cc_final: 0.9066 (t-100) REVERT: C 390 LEU cc_start: 0.9363 (tp) cc_final: 0.8979 (tp) REVERT: C 424 ILE cc_start: 0.9306 (pt) cc_final: 0.9048 (pt) REVERT: C 492 GLU cc_start: 0.7937 (mp0) cc_final: 0.7729 (mp0) REVERT: D 522 PHE cc_start: 0.8996 (t80) cc_final: 0.8579 (t80) REVERT: D 542 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8415 (ttp-110) REVERT: D 579 ARG cc_start: 0.8423 (mtt180) cc_final: 0.7839 (mtp180) REVERT: D 585 ARG cc_start: 0.9118 (mtp-110) cc_final: 0.8672 (mmm-85) REVERT: D 588 ARG cc_start: 0.8807 (ttm170) cc_final: 0.7915 (tmm-80) REVERT: E 33 ASN cc_start: 0.8678 (t0) cc_final: 0.8425 (t0) REVERT: E 72 HIS cc_start: 0.8471 (m-70) cc_final: 0.8042 (m-70) REVERT: E 95 MET cc_start: 0.9160 (ppp) cc_final: 0.8550 (ppp) REVERT: E 97 LYS cc_start: 0.9360 (mtpp) cc_final: 0.9030 (mtpp) REVERT: E 100 MET cc_start: 0.9631 (mtt) cc_final: 0.9324 (mtt) REVERT: E 180 ASP cc_start: 0.8531 (m-30) cc_final: 0.8108 (m-30) REVERT: E 381 GLU cc_start: 0.8627 (tp30) cc_final: 0.8240 (tt0) REVERT: F 567 LYS cc_start: 0.9425 (mttt) cc_final: 0.9000 (mmtm) REVERT: F 596 TRP cc_start: 0.8319 (m-10) cc_final: 0.7588 (m-90) REVERT: F 635 ILE cc_start: 0.8855 (pt) cc_final: 0.8218 (pt) REVERT: F 643 TYR cc_start: 0.9308 (m-10) cc_final: 0.8788 (m-80) REVERT: F 646 LEU cc_start: 0.9541 (mt) cc_final: 0.9201 (mt) REVERT: F 656 ASN cc_start: 0.9032 (m-40) cc_final: 0.8637 (m110) outliers start: 2 outliers final: 0 residues processed: 282 average time/residue: 0.1286 time to fit residues: 53.0104 Evaluate side-chains 225 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 35 optimal weight: 0.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.067894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055990 restraints weight = 75927.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.057567 restraints weight = 44514.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.058653 restraints weight = 30369.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.059389 restraints weight = 22948.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059941 restraints weight = 18678.109| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 15855 Z= 0.155 Angle : 0.732 16.600 21709 Z= 0.349 Chirality : 0.046 0.294 2698 Planarity : 0.004 0.061 2637 Dihedral : 6.552 58.838 3616 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.07 % Allowed : 0.80 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1656 helix: 0.42 (0.26), residues: 416 sheet: -0.06 (0.24), residues: 418 loop : -0.30 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 588 TYR 0.013 0.002 TYR C 484 PHE 0.015 0.001 PHE E 391 TRP 0.075 0.002 TRP D 596 HIS 0.007 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00350 (15744) covalent geometry : angle 0.67491 (21409) SS BOND : bond 0.00485 ( 33) SS BOND : angle 1.61376 ( 66) hydrogen bonds : bond 0.04404 ( 557) hydrogen bonds : angle 4.95716 ( 1671) link_ALPHA1-3 : bond 0.00553 ( 3) link_ALPHA1-3 : angle 2.34690 ( 9) link_BETA1-4 : bond 0.00290 ( 13) link_BETA1-4 : angle 1.92353 ( 39) link_NAG-ASN : bond 0.00443 ( 62) link_NAG-ASN : angle 2.86839 ( 186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.510 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8620 (m-30) cc_final: 0.8372 (m-30) REVERT: A 288 LEU cc_start: 0.9423 (mp) cc_final: 0.9141 (mp) REVERT: B 595 ILE cc_start: 0.9525 (tp) cc_final: 0.9035 (tp) REVERT: B 601 LYS cc_start: 0.9295 (pttm) cc_final: 0.8998 (pttm) REVERT: B 634 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 635 ILE cc_start: 0.9528 (tp) cc_final: 0.8991 (tp) REVERT: B 638 TYR cc_start: 0.8530 (m-80) cc_final: 0.8130 (m-10) REVERT: B 648 GLU cc_start: 0.8919 (pt0) cc_final: 0.8486 (pt0) REVERT: B 650 GLN cc_start: 0.8916 (tp40) cc_final: 0.8551 (tm-30) REVERT: B 654 GLU cc_start: 0.9236 (tp30) cc_final: 0.8574 (tp30) REVERT: B 657 GLU cc_start: 0.8939 (tp30) cc_final: 0.8348 (tp30) REVERT: C 46 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8576 (tttp) REVERT: C 49 GLU cc_start: 0.8335 (tp30) cc_final: 0.8080 (tp30) REVERT: C 80 ASN cc_start: 0.9040 (t0) cc_final: 0.8800 (t0) REVERT: C 95 MET cc_start: 0.9211 (ptm) cc_final: 0.8031 (ppp) REVERT: C 99 ASN cc_start: 0.8793 (p0) cc_final: 0.8355 (p0) REVERT: C 104 MET cc_start: 0.9083 (ptm) cc_final: 0.8796 (ppp) REVERT: C 125 LEU cc_start: 0.9433 (tp) cc_final: 0.9152 (tt) REVERT: C 168 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8883 (mtpt) REVERT: C 271 ILE cc_start: 0.8599 (mt) cc_final: 0.8235 (mt) REVERT: C 316 TRP cc_start: 0.8575 (m100) cc_final: 0.8151 (m100) REVERT: C 338 TRP cc_start: 0.9458 (t-100) cc_final: 0.9179 (t-100) REVERT: C 390 LEU cc_start: 0.9363 (tp) cc_final: 0.9006 (tp) REVERT: C 426 MET cc_start: 0.9068 (tpt) cc_final: 0.8826 (tpp) REVERT: D 522 PHE cc_start: 0.9044 (t80) cc_final: 0.8575 (t80) REVERT: D 542 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8431 (ttp-110) REVERT: D 574 LYS cc_start: 0.9231 (tppp) cc_final: 0.9008 (tppp) REVERT: D 579 ARG cc_start: 0.8217 (mtt180) cc_final: 0.7874 (ttp-170) REVERT: D 585 ARG cc_start: 0.9113 (mtp-110) cc_final: 0.8688 (mmm-85) REVERT: D 586 TYR cc_start: 0.9361 (t80) cc_final: 0.8972 (t80) REVERT: D 588 ARG cc_start: 0.8877 (ttm170) cc_final: 0.8016 (tmm-80) REVERT: E 33 ASN cc_start: 0.8686 (t0) cc_final: 0.8422 (t0) REVERT: E 72 HIS cc_start: 0.8476 (m-70) cc_final: 0.8016 (m-70) REVERT: E 95 MET cc_start: 0.9176 (ppp) cc_final: 0.8711 (ppp) REVERT: E 97 LYS cc_start: 0.9362 (mtpp) cc_final: 0.9043 (mtpp) REVERT: E 100 MET cc_start: 0.9615 (mtt) cc_final: 0.9311 (mtt) REVERT: E 180 ASP cc_start: 0.8521 (m-30) cc_final: 0.8154 (m-30) REVERT: E 381 GLU cc_start: 0.8546 (tp30) cc_final: 0.8290 (tt0) REVERT: F 567 LYS cc_start: 0.9409 (mttt) cc_final: 0.9009 (mmtm) REVERT: F 596 TRP cc_start: 0.8369 (m-10) cc_final: 0.7745 (m-90) REVERT: F 602 LEU cc_start: 0.9272 (mp) cc_final: 0.8891 (mt) REVERT: F 643 TYR cc_start: 0.9344 (m-10) cc_final: 0.8898 (m-80) REVERT: F 646 LEU cc_start: 0.9546 (mt) cc_final: 0.9329 (mt) REVERT: F 656 ASN cc_start: 0.9056 (m-40) cc_final: 0.8692 (m110) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.1202 time to fit residues: 47.1619 Evaluate side-chains 207 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 50 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 72 HIS C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055258 restraints weight = 76985.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056799 restraints weight = 45110.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057864 restraints weight = 30790.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058583 restraints weight = 23222.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.059150 restraints weight = 18941.236| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15855 Z= 0.198 Angle : 0.752 16.137 21709 Z= 0.365 Chirality : 0.046 0.312 2698 Planarity : 0.004 0.052 2637 Dihedral : 6.738 60.225 3616 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1656 helix: 0.45 (0.26), residues: 415 sheet: -0.15 (0.25), residues: 401 loop : -0.39 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 588 TYR 0.024 0.002 TYR A 217 PHE 0.016 0.002 PHE E 391 TRP 0.079 0.003 TRP D 596 HIS 0.008 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00442 (15744) covalent geometry : angle 0.70064 (21409) SS BOND : bond 0.00558 ( 33) SS BOND : angle 1.58205 ( 66) hydrogen bonds : bond 0.04454 ( 557) hydrogen bonds : angle 5.09954 ( 1671) link_ALPHA1-3 : bond 0.00422 ( 3) link_ALPHA1-3 : angle 2.38295 ( 9) link_BETA1-4 : bond 0.00278 ( 13) link_BETA1-4 : angle 1.99652 ( 39) link_NAG-ASN : bond 0.00443 ( 62) link_NAG-ASN : angle 2.75178 ( 186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.535 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8665 (m-30) cc_final: 0.8394 (m-30) REVERT: A 288 LEU cc_start: 0.9426 (mp) cc_final: 0.9145 (mp) REVERT: A 490 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8696 (ttpp) REVERT: B 577 GLN cc_start: 0.9452 (tt0) cc_final: 0.9211 (tt0) REVERT: B 601 LYS cc_start: 0.9274 (pttm) cc_final: 0.9023 (pttm) REVERT: B 634 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 635 ILE cc_start: 0.9525 (tp) cc_final: 0.8976 (tp) REVERT: B 638 TYR cc_start: 0.8483 (m-80) cc_final: 0.8091 (m-10) REVERT: B 657 GLU cc_start: 0.8727 (tp30) cc_final: 0.8355 (tp30) REVERT: C 49 GLU cc_start: 0.8310 (tp30) cc_final: 0.7863 (tp30) REVERT: C 80 ASN cc_start: 0.9037 (t0) cc_final: 0.8766 (t0) REVERT: C 98 ASN cc_start: 0.9294 (t0) cc_final: 0.8893 (t0) REVERT: C 104 MET cc_start: 0.9220 (ptm) cc_final: 0.8903 (ppp) REVERT: C 125 LEU cc_start: 0.9481 (tp) cc_final: 0.9197 (tt) REVERT: C 271 ILE cc_start: 0.8580 (mt) cc_final: 0.8122 (mt) REVERT: C 316 TRP cc_start: 0.8619 (m100) cc_final: 0.8165 (m100) REVERT: C 338 TRP cc_start: 0.9548 (t-100) cc_final: 0.9057 (t-100) REVERT: C 340 GLU cc_start: 0.9178 (pt0) cc_final: 0.8882 (mm-30) REVERT: C 390 LEU cc_start: 0.9380 (tp) cc_final: 0.9031 (tp) REVERT: D 522 PHE cc_start: 0.9058 (t80) cc_final: 0.8538 (t80) REVERT: D 542 ARG cc_start: 0.8709 (ttp-110) cc_final: 0.8397 (ttp-110) REVERT: D 585 ARG cc_start: 0.9168 (mtp-110) cc_final: 0.8698 (mmm-85) REVERT: D 588 ARG cc_start: 0.8868 (ttm170) cc_final: 0.8138 (tmm-80) REVERT: E 33 ASN cc_start: 0.8682 (t0) cc_final: 0.8404 (t0) REVERT: E 72 HIS cc_start: 0.8402 (m-70) cc_final: 0.7927 (m-70) REVERT: E 95 MET cc_start: 0.9195 (ppp) cc_final: 0.8776 (ppp) REVERT: E 97 LYS cc_start: 0.9344 (mtpp) cc_final: 0.9021 (mtpp) REVERT: E 100 MET cc_start: 0.9610 (mtt) cc_final: 0.9321 (mtt) REVERT: E 180 ASP cc_start: 0.8518 (m-30) cc_final: 0.8070 (m-30) REVERT: E 381 GLU cc_start: 0.8571 (tp30) cc_final: 0.8360 (tt0) REVERT: F 567 LYS cc_start: 0.9415 (mttt) cc_final: 0.9028 (mptt) REVERT: F 580 VAL cc_start: 0.9367 (m) cc_final: 0.8669 (m) REVERT: F 584 GLU cc_start: 0.9031 (mt-10) cc_final: 0.7680 (mt-10) REVERT: F 596 TRP cc_start: 0.8395 (m-10) cc_final: 0.7636 (m-90) REVERT: F 601 LYS cc_start: 0.8601 (tptt) cc_final: 0.8310 (tppt) REVERT: F 643 TYR cc_start: 0.9356 (m-10) cc_final: 0.8922 (m-80) REVERT: F 646 LEU cc_start: 0.9540 (mt) cc_final: 0.9203 (mt) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.1215 time to fit residues: 45.7568 Evaluate side-chains 203 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 2 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 151 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056735 restraints weight = 76835.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058337 restraints weight = 44932.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059439 restraints weight = 30494.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060165 restraints weight = 22948.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060746 restraints weight = 18684.496| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15855 Z= 0.133 Angle : 0.719 16.071 21709 Z= 0.349 Chirality : 0.046 0.280 2698 Planarity : 0.004 0.054 2637 Dihedral : 6.337 64.369 3616 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1656 helix: 0.44 (0.26), residues: 408 sheet: -0.08 (0.25), residues: 410 loop : -0.37 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 588 TYR 0.017 0.002 TYR A 217 PHE 0.019 0.001 PHE E 376 TRP 0.078 0.002 TRP D 596 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00295 (15744) covalent geometry : angle 0.66921 (21409) SS BOND : bond 0.00482 ( 33) SS BOND : angle 1.57980 ( 66) hydrogen bonds : bond 0.04295 ( 557) hydrogen bonds : angle 4.96319 ( 1671) link_ALPHA1-3 : bond 0.00535 ( 3) link_ALPHA1-3 : angle 2.15462 ( 9) link_BETA1-4 : bond 0.00331 ( 13) link_BETA1-4 : angle 1.82216 ( 39) link_NAG-ASN : bond 0.00441 ( 62) link_NAG-ASN : angle 2.64762 ( 186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.548 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: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8555 (m-30) cc_final: 0.8282 (m-30) REVERT: A 217 TYR cc_start: 0.8790 (m-10) cc_final: 0.8472 (m-10) REVERT: A 288 LEU cc_start: 0.9425 (mp) cc_final: 0.9105 (mp) REVERT: A 376 PHE cc_start: 0.7836 (m-80) cc_final: 0.7579 (m-80) REVERT: A 490 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8614 (ttpp) REVERT: B 591 GLN cc_start: 0.9269 (tt0) cc_final: 0.8919 (tt0) REVERT: B 596 TRP cc_start: 0.8729 (m-10) cc_final: 0.8487 (m-10) REVERT: B 634 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 635 ILE cc_start: 0.9488 (tp) cc_final: 0.8921 (tp) REVERT: B 638 TYR cc_start: 0.8427 (m-80) cc_final: 0.8080 (m-10) REVERT: B 645 LEU cc_start: 0.9569 (mt) cc_final: 0.9308 (mt) REVERT: B 646 LEU cc_start: 0.9566 (mt) cc_final: 0.9207 (mt) REVERT: B 656 ASN cc_start: 0.8869 (m110) cc_final: 0.8655 (m110) REVERT: B 657 GLU cc_start: 0.8721 (tp30) cc_final: 0.8300 (tp30) REVERT: C 49 GLU cc_start: 0.8399 (tp30) cc_final: 0.8058 (tp30) REVERT: C 80 ASN cc_start: 0.8940 (t0) cc_final: 0.8718 (t0) REVERT: C 95 MET cc_start: 0.9191 (ptm) cc_final: 0.7722 (ppp) REVERT: C 98 ASN cc_start: 0.9285 (t0) cc_final: 0.8696 (t0) REVERT: C 104 MET cc_start: 0.9172 (ptm) cc_final: 0.8909 (ppp) REVERT: C 125 LEU cc_start: 0.9497 (tp) cc_final: 0.9197 (tt) REVERT: C 271 ILE cc_start: 0.8398 (mt) cc_final: 0.8151 (mt) REVERT: C 316 TRP cc_start: 0.8532 (m100) cc_final: 0.8011 (m100) REVERT: C 338 TRP cc_start: 0.9494 (t-100) cc_final: 0.9051 (t-100) REVERT: C 340 GLU cc_start: 0.9164 (pt0) cc_final: 0.8854 (mm-30) REVERT: C 390 LEU cc_start: 0.9340 (tp) cc_final: 0.9001 (tp) REVERT: D 522 PHE cc_start: 0.9029 (t80) cc_final: 0.8509 (t80) REVERT: D 542 ARG cc_start: 0.8665 (ttp-110) cc_final: 0.8367 (ttp-110) REVERT: D 579 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7109 (ttp-170) REVERT: D 585 ARG cc_start: 0.9119 (mtp-110) cc_final: 0.8589 (mmm-85) REVERT: D 586 TYR cc_start: 0.9299 (t80) cc_final: 0.8956 (t80) REVERT: D 588 ARG cc_start: 0.8772 (ttm170) cc_final: 0.8139 (tmm-80) REVERT: D 589 ASP cc_start: 0.9203 (m-30) cc_final: 0.8870 (m-30) REVERT: D 590 GLN cc_start: 0.9248 (mm-40) cc_final: 0.9026 (mm-40) REVERT: E 33 ASN cc_start: 0.8655 (t0) cc_final: 0.8368 (t0) REVERT: E 72 HIS cc_start: 0.8372 (m-70) cc_final: 0.7918 (m-70) REVERT: E 95 MET cc_start: 0.9143 (ppp) cc_final: 0.8772 (ppp) REVERT: E 97 LYS cc_start: 0.9337 (mtpp) cc_final: 0.9069 (mtpp) REVERT: E 100 MET cc_start: 0.9626 (mtt) cc_final: 0.9358 (mtt) REVERT: E 180 ASP cc_start: 0.8428 (m-30) cc_final: 0.8097 (m-30) REVERT: E 381 GLU cc_start: 0.8542 (tp30) cc_final: 0.8272 (tt0) REVERT: E 475 MET cc_start: 0.8549 (mmm) cc_final: 0.8344 (mmm) REVERT: F 567 LYS cc_start: 0.9459 (mttt) cc_final: 0.9032 (mptt) REVERT: F 584 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8258 (mt-10) REVERT: F 591 GLN cc_start: 0.8865 (tt0) cc_final: 0.8622 (tt0) REVERT: F 596 TRP cc_start: 0.8347 (m-10) cc_final: 0.7830 (m-90) REVERT: F 643 TYR cc_start: 0.9313 (m-10) cc_final: 0.8917 (m-80) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.1220 time to fit residues: 48.5385 Evaluate side-chains 212 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 110 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 50 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 174 optimal weight: 20.0000 chunk 78 optimal weight: 0.0010 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 300 ASN B 650 GLN C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.067374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055709 restraints weight = 76899.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057216 restraints weight = 45022.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058303 restraints weight = 30901.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.059031 restraints weight = 23293.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.059611 restraints weight = 18941.583| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15855 Z= 0.180 Angle : 0.730 15.555 21709 Z= 0.356 Chirality : 0.045 0.301 2698 Planarity : 0.004 0.053 2637 Dihedral : 6.464 63.859 3616 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1656 helix: 0.44 (0.26), residues: 408 sheet: -0.16 (0.25), residues: 413 loop : -0.43 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 588 TYR 0.015 0.002 TYR E 217 PHE 0.014 0.002 PHE C 353 TRP 0.077 0.003 TRP D 596 HIS 0.008 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00400 (15744) covalent geometry : angle 0.68021 (21409) SS BOND : bond 0.00523 ( 33) SS BOND : angle 1.58838 ( 66) hydrogen bonds : bond 0.04360 ( 557) hydrogen bonds : angle 5.03974 ( 1671) link_ALPHA1-3 : bond 0.00337 ( 3) link_ALPHA1-3 : angle 2.25710 ( 9) link_BETA1-4 : bond 0.00266 ( 13) link_BETA1-4 : angle 1.95441 ( 39) link_NAG-ASN : bond 0.00419 ( 62) link_NAG-ASN : angle 2.64179 ( 186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.78 seconds wall clock time: 36 minutes 45.49 seconds (2205.49 seconds total)