Starting phenix.real_space_refine on Fri Jul 3 19:14:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l90_23243/07_2026/7l90_23243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l90_23243/07_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_23243/07_2026/7l90_23243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l90_23243/07_2026/7l90_23243.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l90_23243/07_2026/7l90_23243.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l90_23243/07_2026/7l90_23243.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l90_23243/07_2026/7l90_23243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l90_23243/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 3.49, per 1000 atoms: 0.23 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: 1.55 Conformation dependent library (CDL) restraints added in 633.4 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: 0.44 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: 3.04 Time building geometry restraints manager: 2.03 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 - 16.73: 8468 16.73 - 33.47: 265 33.47 - 50.20: 78 50.20 - 66.93: 36 66.93 - 83.67: 17 Dihedral angle restraints: 8864 sinusoidal: 3374 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 8861 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: 3.090 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.360 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 10.812 83.667 5191 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/Z covalent geometry : bond 0.02092 / 1.12 (15744) covalent geometry : angle 1.76273 / 1.14 (21409) SS BOND : bond 0.02683 / 1.97 ( 33) SS BOND : angle 3.07185 / 2.21 ( 66) hydrogen bonds : bond 0.17940 / 12.04 ( 557) hydrogen bonds : angle 7.57642 / 5.20 ( 1671) link_ALPHA1-3 : bond 0.08121 / 3.65 ( 3) link_ALPHA1-3 : angle 5.65982 / 3.45 ( 9) link_BETA1-4 : bond 0.07231 / 4.19 ( 13) link_BETA1-4 : angle 4.84911 / 3.16 ( 39) link_NAG-ASN : bond 0.07717 / 4.97 ( 62) link_NAG-ASN : angle 2.76563 / 1.95 ( 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 : 0.512 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: 0.1311 time to fit residues: 100.8020 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 : 0.473 ------------------------------------------------------------------------------- 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... 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 577 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060251 restraints weight = 72003.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062165 restraints weight = 39396.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063483 restraints weight = 25598.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.064388 restraints weight = 18679.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065039 restraints weight = 14727.609| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15855 Z= 0.185 Angle : 0.881 14.949 21709 Z= 0.426 Chirality : 0.051 0.418 2698 Planarity : 0.004 0.083 2637 Dihedral : 5.245 23.352 1990 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.40 % Allowed : 2.85 % Favored : 96.75 % 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: 0.81 (0.20), residues: 1656 helix: 0.85 (0.25), residues: 412 sheet: 0.86 (0.24), residues: 435 loop : 0.34 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 166 TYR 0.027 0.002 TYR F 643 PHE 0.017 0.002 PHE A 353 TRP 0.034 0.003 TRP F 571 HIS 0.007 0.001 HIS D 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (15744) covalent geometry : angle 0.80795 / 0.41 (21409) SS BOND : bond 0.00279 / 0.20 ( 33) SS BOND : angle 1.49579 / 1.11 ( 66) hydrogen bonds : bond 0.06678 / 4.47 ( 557) hydrogen bonds : angle 5.74057 / 3.94 ( 1671) link_ALPHA1-3 : bond 0.01131 / 0.57 ( 3) link_ALPHA1-3 : angle 2.68729 / 1.62 ( 9) link_BETA1-4 : bond 0.00922 / 0.47 ( 13) link_BETA1-4 : angle 2.89666 / 1.84 ( 39) link_NAG-ASN : bond 0.00628 / 0.40 ( 62) link_NAG-ASN : angle 3.53978 / 2.48 ( 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: 6 poor density : 371 time to evaluate : 0.577 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: A 35 TRP cc_start: 0.8729 (m100) cc_final: 0.8042 (m100) REVERT: A 98 ASN cc_start: 0.8353 (t0) cc_final: 0.8145 (t0) REVERT: A 104 MET cc_start: 0.9145 (tpp) cc_final: 0.8929 (mmm) REVERT: A 109 ILE cc_start: 0.9536 (tt) cc_final: 0.9212 (pt) REVERT: A 114 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 123 THR cc_start: 0.9580 (m) cc_final: 0.9332 (m) REVERT: A 288 LEU cc_start: 0.9566 (mp) cc_final: 0.9273 (mp) REVERT: A 356 ASN cc_start: 0.7570 (t0) cc_final: 0.7112 (p0) REVERT: A 452 LEU cc_start: 0.9487 (mt) cc_final: 0.9188 (mt) REVERT: B 602 LEU cc_start: 0.8960 (mt) cc_final: 0.8631 (pt) REVERT: B 603 ILE cc_start: 0.8707 (mt) cc_final: 0.8410 (tp) REVERT: B 634 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 635 ILE cc_start: 0.9531 (tp) cc_final: 0.9290 (tp) REVERT: B 650 GLN cc_start: 0.8882 (tp40) cc_final: 0.8413 (tm-30) REVERT: B 654 GLU cc_start: 0.9207 (tp30) cc_final: 0.8795 (tp30) REVERT: C 46 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8533 (mmmt) REVERT: C 95 MET cc_start: 0.9214 (ptt) cc_final: 0.8720 (ptt) REVERT: C 98 ASN cc_start: 0.8930 (t0) cc_final: 0.8465 (t0) REVERT: C 100 MET cc_start: 0.9175 (mtm) cc_final: 0.8766 (mtm) REVERT: C 116 LEU cc_start: 0.9557 (pp) cc_final: 0.9335 (tp) REVERT: C 168 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8386 (mtmt) REVERT: C 316 TRP cc_start: 0.8435 (m100) cc_final: 0.7866 (m100) REVERT: C 338 TRP cc_start: 0.9532 (t-100) cc_final: 0.9202 (t-100) REVERT: C 374 HIS cc_start: 0.9043 (t70) cc_final: 0.8654 (t70) REVERT: C 390 LEU cc_start: 0.9406 (tp) cc_final: 0.8686 (tp) REVERT: C 391 PHE cc_start: 0.8922 (m-80) cc_final: 0.8294 (m-10) REVERT: C 477 ASP cc_start: 0.9551 (m-30) cc_final: 0.9086 (m-30) REVERT: D 522 PHE cc_start: 0.8244 (t80) cc_final: 0.7496 (t80) REVERT: D 536 THR cc_start: 0.9338 (p) cc_final: 0.9114 (p) REVERT: D 538 THR cc_start: 0.9425 (p) cc_final: 0.9120 (t) REVERT: D 579 ARG cc_start: 0.8339 (mtt180) cc_final: 0.7635 (mtp180) REVERT: D 586 TYR cc_start: 0.9230 (t80) cc_final: 0.8472 (t80) REVERT: D 588 ARG cc_start: 0.8908 (ttp-170) cc_final: 0.8250 (tmm-80) REVERT: D 589 ASP cc_start: 0.9235 (m-30) cc_final: 0.8963 (m-30) REVERT: D 595 ILE cc_start: 0.9663 (mm) cc_final: 0.9304 (tp) REVERT: D 596 TRP cc_start: 0.8320 (m-10) cc_final: 0.7939 (m-90) REVERT: D 603 ILE cc_start: 0.9140 (tt) cc_final: 0.8797 (mm) REVERT: D 628 TRP cc_start: 0.7495 (t-100) cc_final: 0.6781 (t-100) REVERT: D 631 TRP cc_start: 0.8511 (t-100) cc_final: 0.8276 (t-100) REVERT: E 39 TYR cc_start: 0.8804 (m-80) cc_final: 0.8574 (m-80) REVERT: E 72 HIS cc_start: 0.8810 (m-70) cc_final: 0.8324 (m-70) REVERT: E 97 LYS cc_start: 0.9366 (mtpp) cc_final: 0.9125 (mtpp) REVERT: E 104 MET cc_start: 0.9332 (ttm) cc_final: 0.9088 (ttp) REVERT: E 141 ASP cc_start: 0.8911 (m-30) cc_final: 0.8656 (p0) REVERT: E 180 ASP cc_start: 0.8420 (m-30) cc_final: 0.8043 (m-30) REVERT: E 260 LEU cc_start: 0.9088 (mp) cc_final: 0.8886 (mp) REVERT: E 489 VAL cc_start: 0.9047 (m) cc_final: 0.8584 (m) REVERT: F 567 LYS cc_start: 0.9272 (mttt) cc_final: 0.8901 (mmtm) REVERT: F 577 GLN cc_start: 0.9331 (tt0) cc_final: 0.8974 (tp40) REVERT: F 591 GLN cc_start: 0.8809 (tt0) cc_final: 0.7814 (tt0) REVERT: F 601 LYS cc_start: 0.9021 (mmpt) cc_final: 0.8394 (mtpp) REVERT: F 602 LEU cc_start: 0.9587 (mt) cc_final: 0.9134 (mt) REVERT: F 633 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8594 (mttm) REVERT: F 650 GLN cc_start: 0.8874 (tp40) cc_final: 0.8391 (tm-30) outliers start: 6 outliers final: 1 residues processed: 376 average time/residue: 0.1325 time to fit residues: 72.7229 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 : 0.406 ------------------------------------------------------------------------------- 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: 0.9980 chunk 141 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 170 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS B 540 GLN B 658 GLN C 249 HIS C 352 HIS ** D 540 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058344 restraints weight = 72612.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060185 restraints weight = 40013.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061445 restraints weight = 26280.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.062199 restraints weight = 19405.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062913 restraints weight = 15937.451| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15855 Z= 0.169 Angle : 0.741 10.991 21709 Z= 0.365 Chirality : 0.047 0.293 2698 Planarity : 0.004 0.070 2637 Dihedral : 4.975 22.330 1990 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % 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: 0.54 (0.20), residues: 1656 helix: 0.64 (0.26), residues: 418 sheet: 0.71 (0.24), residues: 434 loop : 0.15 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 166 TYR 0.021 0.002 TYR F 643 PHE 0.014 0.002 PHE D 522 TRP 0.034 0.002 TRP A 427 HIS 0.007 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (15744) covalent geometry : angle 0.69180 / 0.36 (21409) SS BOND : bond 0.00270 / 0.18 ( 33) SS BOND : angle 1.29556 / 0.99 ( 66) hydrogen bonds : bond 0.05463 / 3.66 ( 557) hydrogen bonds : angle 5.25690 / 3.62 ( 1671) link_ALPHA1-3 : bond 0.00883 / 0.43 ( 3) link_ALPHA1-3 : angle 2.64325 / 1.57 ( 9) link_BETA1-4 : bond 0.00538 / 0.29 ( 13) link_BETA1-4 : angle 2.24190 / 1.43 ( 39) link_NAG-ASN : bond 0.00486 / 0.30 ( 62) link_NAG-ASN : angle 2.63573 / 1.83 ( 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 330 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 0.554 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: 0.8666 (m100) cc_final: 0.8266 (m100) REVERT: A 53 PHE cc_start: 0.7881 (m-80) cc_final: 0.7531 (m-80) REVERT: A 98 ASN cc_start: 0.8585 (t0) cc_final: 0.8312 (t0) REVERT: A 104 MET cc_start: 0.9070 (tpp) cc_final: 0.8796 (mmm) REVERT: A 114 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8826 (tm-30) REVERT: A 123 THR cc_start: 0.9458 (m) cc_final: 0.9250 (m) REVERT: A 288 LEU cc_start: 0.9581 (mp) cc_final: 0.9251 (mp) REVERT: A 356 ASN cc_start: 0.7528 (t0) cc_final: 0.6999 (p0) REVERT: B 596 TRP cc_start: 0.9132 (m-10) cc_final: 0.8833 (m-10) REVERT: B 602 LEU cc_start: 0.8736 (mt) cc_final: 0.8481 (pt) REVERT: B 634 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7829 (tm-30) REVERT: B 635 ILE cc_start: 0.9517 (tp) cc_final: 0.9188 (tp) REVERT: B 646 LEU cc_start: 0.9512 (mt) cc_final: 0.9159 (mt) REVERT: B 650 GLN cc_start: 0.8827 (tp40) cc_final: 0.8512 (tm-30) REVERT: C 40 TYR cc_start: 0.8247 (t80) cc_final: 0.7987 (t80) REVERT: C 46 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8537 (mmmt) REVERT: C 95 MET cc_start: 0.9155 (ptt) cc_final: 0.8730 (ptt) REVERT: C 98 ASN cc_start: 0.9011 (t0) cc_final: 0.8760 (t0) REVERT: C 168 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8467 (mtmt) REVERT: C 316 TRP cc_start: 0.8481 (m100) cc_final: 0.8080 (m100) REVERT: C 338 TRP cc_start: 0.9445 (t-100) cc_final: 0.9175 (t-100) REVERT: C 390 LEU cc_start: 0.9388 (tp) cc_final: 0.8941 (tp) REVERT: C 449 ILE cc_start: 0.8834 (mt) cc_final: 0.8582 (tt) REVERT: C 475 MET cc_start: 0.8418 (mmm) cc_final: 0.7029 (mmm) REVERT: C 477 ASP cc_start: 0.9367 (m-30) cc_final: 0.8914 (m-30) REVERT: C 479 TRP cc_start: 0.8635 (m-10) cc_final: 0.8358 (m-90) REVERT: D 577 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8878 (tm-30) REVERT: D 579 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7843 (mtp180) REVERT: D 585 ARG cc_start: 0.8934 (mtp-110) cc_final: 0.8211 (ptm160) REVERT: D 586 TYR cc_start: 0.9391 (t80) cc_final: 0.8999 (t80) REVERT: D 588 ARG cc_start: 0.8909 (ttp-170) cc_final: 0.8156 (tmm-80) REVERT: D 589 ASP cc_start: 0.9265 (m-30) cc_final: 0.8641 (m-30) REVERT: D 595 ILE cc_start: 0.9680 (mm) cc_final: 0.9122 (tp) REVERT: D 603 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (tt) REVERT: D 650 GLN cc_start: 0.9725 (tp40) cc_final: 0.9230 (tp40) REVERT: E 33 ASN cc_start: 0.8532 (t0) cc_final: 0.8307 (t0) REVERT: E 72 HIS cc_start: 0.8816 (m-70) cc_final: 0.8364 (m-70) REVERT: E 95 MET cc_start: 0.8737 (ptt) cc_final: 0.8423 (ptm) REVERT: E 97 LYS cc_start: 0.9438 (mtpp) cc_final: 0.9209 (mtpp) REVERT: E 161 MET cc_start: 0.9019 (tpp) cc_final: 0.8819 (tpt) REVERT: E 180 ASP cc_start: 0.8336 (m-30) cc_final: 0.7983 (m-30) REVERT: E 260 LEU cc_start: 0.9179 (mp) cc_final: 0.8902 (mp) REVERT: F 543 ASN cc_start: 0.8315 (m-40) cc_final: 0.8037 (m110) REVERT: F 567 LYS cc_start: 0.9295 (mttt) cc_final: 0.8965 (mmtm) REVERT: F 580 VAL cc_start: 0.9399 (m) cc_final: 0.9097 (m) REVERT: F 584 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8022 (mt-10) REVERT: F 595 ILE cc_start: 0.9809 (mm) cc_final: 0.9547 (tp) REVERT: F 596 TRP cc_start: 0.8466 (m-10) cc_final: 0.7779 (m-90) REVERT: F 643 TYR cc_start: 0.9284 (m-10) cc_final: 0.8670 (m-10) REVERT: F 654 GLU cc_start: 0.8945 (tm-30) cc_final: 0.7841 (tm-30) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.1225 time to fit residues: 59.4809 Evaluate side-chains 244 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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: 9.9990 chunk 120 optimal weight: 8.9990 chunk 16 optimal weight: 0.0050 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS C 99 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** D 540 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 = 0.3341 r_free = 0.3341 target = 0.072192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059703 restraints weight = 73197.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061420 restraints weight = 42522.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.062613 restraints weight = 28827.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063405 restraints weight = 21698.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064019 restraints weight = 17660.771| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15855 Z= 0.125 Angle : 0.682 11.010 21709 Z= 0.333 Chirality : 0.046 0.270 2698 Planarity : 0.004 0.066 2637 Dihedral : 4.806 21.856 1990 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % 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: 0.36 (0.20), residues: 1656 helix: 0.51 (0.25), residues: 421 sheet: 0.61 (0.24), residues: 439 loop : -0.00 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 617 TYR 0.023 0.002 TYR D 643 PHE 0.026 0.002 PHE E 376 TRP 0.038 0.002 TRP D 596 HIS 0.006 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (15744) covalent geometry : angle 0.63664 / 0.32 (21409) SS BOND : bond 0.00246 / 0.18 ( 33) SS BOND : angle 0.96087 / 0.72 ( 66) hydrogen bonds : bond 0.04806 / 3.21 ( 557) hydrogen bonds : angle 5.02357 / 3.47 ( 1671) link_ALPHA1-3 : bond 0.00708 / 0.35 ( 3) link_ALPHA1-3 : angle 2.45613 / 1.44 ( 9) link_BETA1-4 : bond 0.00530 / 0.30 ( 13) link_BETA1-4 : angle 1.92345 / 1.25 ( 39) link_NAG-ASN : bond 0.00486 / 0.30 ( 62) link_NAG-ASN : angle 2.50975 / 1.82 ( 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 338 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 0.605 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 35 TRP cc_start: 0.8666 (m100) cc_final: 0.8241 (m100) REVERT: A 104 MET cc_start: 0.9044 (tpp) cc_final: 0.8711 (tpp) REVERT: A 114 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8849 (tm-30) REVERT: A 288 LEU cc_start: 0.9518 (mp) cc_final: 0.9188 (mp) REVERT: A 356 ASN cc_start: 0.7551 (t0) cc_final: 0.7019 (p0) REVERT: A 359 ILE cc_start: 0.7975 (mt) cc_final: 0.7743 (mp) REVERT: A 452 LEU cc_start: 0.9412 (mt) cc_final: 0.8975 (mp) REVERT: B 596 TRP cc_start: 0.9009 (m-10) cc_final: 0.8754 (m-10) REVERT: B 602 LEU cc_start: 0.8784 (mt) cc_final: 0.8577 (pt) REVERT: B 634 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 635 ILE cc_start: 0.9460 (tp) cc_final: 0.9121 (tp) REVERT: B 646 LEU cc_start: 0.9570 (mt) cc_final: 0.9256 (mt) REVERT: B 650 GLN cc_start: 0.8891 (tp40) cc_final: 0.8556 (tm-30) REVERT: C 40 TYR cc_start: 0.8183 (t80) cc_final: 0.7736 (t80) REVERT: C 46 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8396 (mmmt) REVERT: C 95 MET cc_start: 0.9142 (ptt) cc_final: 0.8730 (ptt) REVERT: C 98 ASN cc_start: 0.9041 (t0) cc_final: 0.8818 (t0) REVERT: C 116 LEU cc_start: 0.9506 (pp) cc_final: 0.9300 (tt) REVERT: C 125 LEU cc_start: 0.9468 (tp) cc_final: 0.9228 (tt) REVERT: C 168 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8484 (mtmt) REVERT: C 254 VAL cc_start: 0.9211 (t) cc_final: 0.8937 (m) REVERT: C 316 TRP cc_start: 0.8511 (m100) cc_final: 0.7997 (m100) REVERT: C 475 MET cc_start: 0.8357 (mmm) cc_final: 0.7019 (mmm) REVERT: C 477 ASP cc_start: 0.9319 (m-30) cc_final: 0.8909 (m-30) REVERT: C 479 TRP cc_start: 0.8472 (m-10) cc_final: 0.7961 (m-90) REVERT: D 577 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8827 (tm-30) REVERT: D 579 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7960 (mtp180) REVERT: D 585 ARG cc_start: 0.8893 (mtp-110) cc_final: 0.8349 (ptm160) REVERT: D 586 TYR cc_start: 0.9259 (t80) cc_final: 0.8936 (t80) REVERT: D 588 ARG cc_start: 0.8776 (ttp-170) cc_final: 0.8030 (ttp80) REVERT: D 626 MET cc_start: 0.8528 (tpp) cc_final: 0.8154 (tpp) REVERT: D 650 GLN cc_start: 0.9712 (tp40) cc_final: 0.9473 (tt0) REVERT: E 39 TYR cc_start: 0.8753 (m-80) cc_final: 0.8510 (m-10) REVERT: E 72 HIS cc_start: 0.8792 (m-70) cc_final: 0.7530 (m-70) REVERT: E 95 MET cc_start: 0.8776 (ptt) cc_final: 0.8187 (ppp) REVERT: E 97 LYS cc_start: 0.9362 (mtpp) cc_final: 0.9039 (mtpp) REVERT: E 180 ASP cc_start: 0.8316 (m-30) cc_final: 0.7742 (m-30) REVERT: F 567 LYS cc_start: 0.9313 (mttt) cc_final: 0.8933 (mmtm) REVERT: F 573 ILE cc_start: 0.9151 (mt) cc_final: 0.8818 (mm) REVERT: F 576 LEU cc_start: 0.9276 (mm) cc_final: 0.9037 (pp) REVERT: F 580 VAL cc_start: 0.9317 (m) cc_final: 0.8917 (m) REVERT: F 584 GLU cc_start: 0.9019 (mt-10) cc_final: 0.7702 (mt-10) REVERT: F 595 ILE cc_start: 0.9757 (mm) cc_final: 0.9331 (tt) REVERT: F 596 TRP cc_start: 0.8493 (m-10) cc_final: 0.8088 (m-10) REVERT: F 643 TYR cc_start: 0.9286 (m-10) cc_final: 0.9075 (m-80) REVERT: F 653 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8622 (tm-30) REVERT: F 654 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8695 (tm-30) REVERT: F 661 LEU cc_start: 0.8096 (tp) cc_final: 0.7829 (tt) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.1219 time to fit residues: 61.0803 Evaluate side-chains 243 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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: 7.9990 chunk 34 optimal weight: 8.9990 chunk 182 optimal weight: 40.0000 chunk 85 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 181 optimal weight: 40.0000 chunk 129 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN E 352 HIS E 432 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.054176 restraints weight = 78628.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.055689 restraints weight = 46209.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056723 restraints weight = 31622.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057495 restraints weight = 24098.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058040 restraints weight = 19602.314| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 15855 Z= 0.338 Angle : 0.950 11.941 21709 Z= 0.460 Chirality : 0.051 0.380 2698 Planarity : 0.005 0.057 2637 Dihedral : 5.472 23.589 1990 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.07 % Allowed : 2.59 % Favored : 97.35 % 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: -0.21 (0.20), residues: 1656 helix: 0.09 (0.25), residues: 421 sheet: 0.04 (0.23), residues: 445 loop : -0.22 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 456 TYR 0.020 0.003 TYR D 643 PHE 0.025 0.003 PHE E 391 TRP 0.057 0.003 TRP D 596 HIS 0.013 0.002 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.34 (15744) covalent geometry : angle 0.90257 / 0.45 (21409) SS BOND : bond 0.00868 / 0.61 ( 33) SS BOND : angle 1.63480 / 1.18 ( 66) hydrogen bonds : bond 0.05532 / 3.69 ( 557) hydrogen bonds : angle 5.52012 / 3.82 ( 1671) link_ALPHA1-3 : bond 0.00389 / 0.18 ( 3) link_ALPHA1-3 : angle 2.64181 / 1.59 ( 9) link_BETA1-4 : bond 0.00382 / 0.22 ( 13) link_BETA1-4 : angle 2.58256 / 1.67 ( 39) link_NAG-ASN : bond 0.00700 / 0.43 ( 62) link_NAG-ASN : angle 2.99310 / 2.08 ( 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 270 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.571 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 35 TRP cc_start: 0.8850 (m100) cc_final: 0.8306 (m100) REVERT: A 104 MET cc_start: 0.8950 (tpp) cc_final: 0.8746 (mmm) REVERT: A 426 MET cc_start: 0.9211 (tpp) cc_final: 0.8890 (tpp) REVERT: A 490 LYS cc_start: 0.9187 (ttpt) cc_final: 0.8640 (ttpp) REVERT: B 634 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 635 ILE cc_start: 0.9584 (tp) cc_final: 0.9156 (tp) REVERT: C 46 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8393 (mmtm) REVERT: C 91 GLU cc_start: 0.8308 (tp30) cc_final: 0.8094 (tp30) REVERT: C 168 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8881 (mtpt) REVERT: C 316 TRP cc_start: 0.8726 (m100) cc_final: 0.8452 (m100) REVERT: C 390 LEU cc_start: 0.9403 (tp) cc_final: 0.9027 (tp) REVERT: C 426 MET cc_start: 0.9207 (tpt) cc_final: 0.8465 (tpp) REVERT: C 475 MET cc_start: 0.8433 (mmm) cc_final: 0.7799 (mmm) REVERT: C 477 ASP cc_start: 0.9273 (m-30) cc_final: 0.9060 (m-30) REVERT: C 484 TYR cc_start: 0.8964 (p90) cc_final: 0.8738 (p90) REVERT: D 574 LYS cc_start: 0.9220 (tppp) cc_final: 0.8937 (tppp) REVERT: D 577 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8738 (tm-30) REVERT: D 579 ARG cc_start: 0.8365 (mtt180) cc_final: 0.7993 (mtp180) REVERT: D 581 LEU cc_start: 0.9452 (tt) cc_final: 0.9196 (tp) REVERT: D 588 ARG cc_start: 0.8979 (ttp-170) cc_final: 0.8174 (tmm-80) REVERT: E 33 ASN cc_start: 0.8648 (t0) cc_final: 0.8432 (t0) REVERT: E 72 HIS cc_start: 0.8758 (m-70) cc_final: 0.7989 (m-70) REVERT: E 97 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9112 (mtpp) REVERT: E 180 ASP cc_start: 0.8703 (m-30) cc_final: 0.8371 (m-30) REVERT: E 260 LEU cc_start: 0.9368 (mp) cc_final: 0.9162 (mp) REVERT: F 567 LYS cc_start: 0.9434 (mttt) cc_final: 0.9034 (mmtm) REVERT: F 595 ILE cc_start: 0.9769 (mm) cc_final: 0.9535 (tt) REVERT: F 596 TRP cc_start: 0.8881 (m-10) cc_final: 0.7935 (m-10) REVERT: F 626 MET cc_start: 0.8141 (tmm) cc_final: 0.7693 (tmm) REVERT: F 635 ILE cc_start: 0.8992 (pt) cc_final: 0.8684 (pt) REVERT: F 643 TYR cc_start: 0.9450 (m-10) cc_final: 0.8797 (m-80) REVERT: F 646 LEU cc_start: 0.9506 (mt) cc_final: 0.9295 (mt) REVERT: F 653 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8747 (tm-30) REVERT: F 654 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8634 (tm-30) REVERT: F 661 LEU cc_start: 0.8303 (tp) cc_final: 0.8060 (tt) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.1196 time to fit residues: 48.3534 Evaluate side-chains 197 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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: 4.9990 chunk 67 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 182 optimal weight: 40.0000 chunk 58 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.067983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.055765 restraints weight = 76852.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.057355 restraints weight = 45141.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058458 restraints weight = 30926.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059203 restraints weight = 23491.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.059776 restraints weight = 19267.506| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5597 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 : 0.744 12.269 21709 Z= 0.358 Chirality : 0.047 0.460 2698 Planarity : 0.004 0.059 2637 Dihedral : 5.104 23.743 1990 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.13 % Allowed : 1.92 % Favored : 97.94 % 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: 0.36 (0.26), residues: 417 sheet: 0.12 (0.24), residues: 420 loop : -0.32 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 588 TYR 0.024 0.002 TYR D 643 PHE 0.030 0.002 PHE E 376 TRP 0.061 0.003 TRP D 596 HIS 0.009 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (15744) covalent geometry : angle 0.69233 / 0.35 (21409) SS BOND : bond 0.00390 / 0.27 ( 33) SS BOND : angle 1.10571 / 0.74 ( 66) hydrogen bonds : bond 0.04997 / 3.37 ( 557) hydrogen bonds : angle 5.19427 / 3.57 ( 1671) link_ALPHA1-3 : bond 0.00417 / 0.21 ( 3) link_ALPHA1-3 : angle 2.38427 / 1.38 ( 9) link_BETA1-4 : bond 0.00268 / 0.17 ( 13) link_BETA1-4 : angle 1.97625 / 1.29 ( 39) link_NAG-ASN : bond 0.00484 / 0.29 ( 62) link_NAG-ASN : angle 2.79681 / 2.02 ( 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 275 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 0.597 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: A 35 TRP cc_start: 0.8785 (m100) cc_final: 0.8395 (m100) REVERT: A 104 MET cc_start: 0.8878 (tpp) cc_final: 0.8608 (mmm) REVERT: A 180 ASP cc_start: 0.8655 (m-30) cc_final: 0.8387 (m-30) REVERT: A 288 LEU cc_start: 0.9478 (mp) cc_final: 0.9265 (mp) REVERT: A 490 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8881 (ttpp) REVERT: B 601 LYS cc_start: 0.9239 (pttm) cc_final: 0.8902 (pttm) REVERT: B 634 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 635 ILE cc_start: 0.9583 (tp) cc_final: 0.9125 (tp) REVERT: C 46 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8205 (mmtm) REVERT: C 49 GLU cc_start: 0.8518 (tp30) cc_final: 0.8267 (tp30) REVERT: C 80 ASN cc_start: 0.8981 (t0) cc_final: 0.8689 (t0) REVERT: C 95 MET cc_start: 0.8853 (ppp) cc_final: 0.8429 (ppp) REVERT: C 168 LYS cc_start: 0.9234 (mmtt) cc_final: 0.8879 (mtpt) REVERT: C 203 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8881 (pp30) REVERT: C 271 ILE cc_start: 0.8790 (mt) cc_final: 0.8344 (mt) REVERT: C 316 TRP cc_start: 0.8675 (m100) cc_final: 0.8325 (m100) REVERT: C 390 LEU cc_start: 0.9467 (tp) cc_final: 0.8970 (tp) REVERT: C 424 ILE cc_start: 0.9378 (pt) cc_final: 0.9098 (pt) REVERT: C 484 TYR cc_start: 0.8872 (p90) cc_final: 0.8659 (p90) REVERT: C 502 LYS cc_start: 0.9236 (tttp) cc_final: 0.9032 (tmtt) REVERT: D 577 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 579 ARG cc_start: 0.8311 (mtt180) cc_final: 0.8001 (mtp180) REVERT: D 585 ARG cc_start: 0.9053 (mtp-110) cc_final: 0.8620 (mmm-85) REVERT: D 588 ARG cc_start: 0.8941 (ttp-170) cc_final: 0.8141 (tmm-80) REVERT: D 595 ILE cc_start: 0.9639 (tp) cc_final: 0.9049 (tp) REVERT: E 33 ASN cc_start: 0.8675 (t0) cc_final: 0.8442 (t0) REVERT: E 72 HIS cc_start: 0.8682 (m-70) cc_final: 0.7681 (m-70) REVERT: E 95 MET cc_start: 0.9228 (ppp) cc_final: 0.8660 (ppp) REVERT: E 97 LYS cc_start: 0.9387 (mtpp) cc_final: 0.8986 (mtpp) REVERT: E 100 MET cc_start: 0.9642 (mtt) cc_final: 0.9382 (mtt) REVERT: E 180 ASP cc_start: 0.8691 (m-30) cc_final: 0.8286 (m-30) REVERT: E 381 GLU cc_start: 0.8600 (tp30) cc_final: 0.8382 (tt0) REVERT: F 530 MET cc_start: 0.7917 (mtm) cc_final: 0.7552 (mtp) REVERT: F 567 LYS cc_start: 0.9427 (mttt) cc_final: 0.9017 (mmtm) REVERT: F 585 ARG cc_start: 0.8808 (ttm-80) cc_final: 0.8582 (ttm-80) REVERT: F 596 TRP cc_start: 0.8696 (m-10) cc_final: 0.7780 (m-10) REVERT: F 601 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8707 (ttmt) REVERT: F 626 MET cc_start: 0.8303 (tmm) cc_final: 0.8032 (tmm) REVERT: F 643 TYR cc_start: 0.9393 (m-10) cc_final: 0.8786 (m-80) REVERT: F 653 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8807 (tm-30) REVERT: F 654 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8716 (tm-30) REVERT: F 661 LEU cc_start: 0.8271 (tp) cc_final: 0.8015 (tt) outliers start: 2 outliers final: 0 residues processed: 275 average time/residue: 0.1215 time to fit residues: 49.4073 Evaluate side-chains 210 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 7.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 0.0020 chunk 154 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** 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 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057243 restraints weight = 75789.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058883 restraints weight = 44637.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060010 restraints weight = 30449.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060818 restraints weight = 23036.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061397 restraints weight = 18684.858| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 15855 Z= 0.135 Angle : 0.722 19.071 21709 Z= 0.346 Chirality : 0.046 0.322 2698 Planarity : 0.004 0.049 2637 Dihedral : 4.889 22.363 1990 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.07 % Allowed : 1.53 % Favored : 98.41 % 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: -0.09 (0.20), residues: 1656 helix: 0.40 (0.26), residues: 420 sheet: 0.12 (0.24), residues: 425 loop : -0.29 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 588 TYR 0.013 0.001 TYR E 217 PHE 0.015 0.001 PHE E 391 TRP 0.073 0.002 TRP D 596 HIS 0.005 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (15744) covalent geometry : angle 0.67036 / 0.33 (21409) SS BOND : bond 0.00467 / 0.29 ( 33) SS BOND : angle 1.85117 / 1.47 ( 66) hydrogen bonds : bond 0.04552 / 3.04 ( 557) hydrogen bonds : angle 5.00360 / 3.45 ( 1671) link_ALPHA1-3 : bond 0.00519 / 0.26 ( 3) link_ALPHA1-3 : angle 2.29193 / 1.32 ( 9) link_BETA1-4 : bond 0.00364 / 0.22 ( 13) link_BETA1-4 : angle 1.75809 / 1.14 ( 39) link_NAG-ASN : bond 0.00470 / 0.27 ( 62) link_NAG-ASN : angle 2.63218 / 1.93 ( 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 296 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.572 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: A 288 LEU cc_start: 0.9452 (mp) cc_final: 0.9191 (mp) REVERT: A 475 MET cc_start: 0.8659 (mmm) cc_final: 0.7382 (mmm) REVERT: A 490 LYS cc_start: 0.9134 (ttpt) cc_final: 0.8455 (ttpp) REVERT: B 577 GLN cc_start: 0.9435 (tt0) cc_final: 0.9223 (tt0) REVERT: B 601 LYS cc_start: 0.9282 (pttm) cc_final: 0.8971 (pttm) REVERT: B 634 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 635 ILE cc_start: 0.9551 (tp) cc_final: 0.9066 (tp) REVERT: B 646 LEU cc_start: 0.9505 (mt) cc_final: 0.9266 (mt) REVERT: B 650 GLN cc_start: 0.8890 (tp40) cc_final: 0.8469 (tm-30) REVERT: B 656 ASN cc_start: 0.8986 (m110) cc_final: 0.8774 (m110) REVERT: C 46 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8280 (mmtm) REVERT: C 49 GLU cc_start: 0.8568 (tp30) cc_final: 0.8241 (tp30) REVERT: C 80 ASN cc_start: 0.9018 (t0) cc_final: 0.8728 (t0) REVERT: C 95 MET cc_start: 0.8766 (ppp) cc_final: 0.8387 (ppp) REVERT: C 168 LYS cc_start: 0.9226 (mmtt) cc_final: 0.8836 (mtpt) REVERT: C 271 ILE cc_start: 0.8727 (mt) cc_final: 0.8263 (mt) REVERT: C 316 TRP cc_start: 0.8560 (m100) cc_final: 0.8029 (m100) REVERT: C 390 LEU cc_start: 0.9448 (tp) cc_final: 0.8991 (tp) REVERT: C 424 ILE cc_start: 0.9259 (pt) cc_final: 0.9033 (pt) REVERT: C 484 TYR cc_start: 0.8882 (p90) cc_final: 0.8625 (p90) REVERT: D 577 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 579 ARG cc_start: 0.8367 (mtt180) cc_final: 0.7898 (mtp180) REVERT: D 585 ARG cc_start: 0.9066 (mtp-110) cc_final: 0.8542 (mmm-85) REVERT: D 586 TYR cc_start: 0.9283 (t80) cc_final: 0.8855 (t80) REVERT: D 588 ARG cc_start: 0.8910 (ttp-170) cc_final: 0.8184 (tmm-80) REVERT: D 590 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8645 (mp10) REVERT: D 595 ILE cc_start: 0.9387 (tp) cc_final: 0.9178 (tp) REVERT: E 33 ASN cc_start: 0.8639 (t0) cc_final: 0.8379 (t0) REVERT: E 72 HIS cc_start: 0.8659 (m-70) cc_final: 0.7716 (m-70) REVERT: E 95 MET cc_start: 0.9176 (ppp) cc_final: 0.8560 (ppp) REVERT: E 97 LYS cc_start: 0.9379 (mtpp) cc_final: 0.9021 (mtpp) REVERT: E 100 MET cc_start: 0.9662 (mtt) cc_final: 0.9385 (mtt) REVERT: E 180 ASP cc_start: 0.8525 (m-30) cc_final: 0.7967 (m-30) REVERT: E 381 GLU cc_start: 0.8598 (tp30) cc_final: 0.8329 (tt0) REVERT: F 567 LYS cc_start: 0.9419 (mttt) cc_final: 0.9012 (mmtm) REVERT: F 596 TRP cc_start: 0.8564 (m-10) cc_final: 0.7655 (m-10) REVERT: F 643 TYR cc_start: 0.9359 (m-10) cc_final: 0.8830 (m-80) REVERT: F 653 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8945 (tm-30) REVERT: F 656 ASN cc_start: 0.9134 (m-40) cc_final: 0.8752 (m110) REVERT: F 661 LEU cc_start: 0.8157 (tp) cc_final: 0.7891 (tt) outliers start: 1 outliers final: 0 residues processed: 296 average time/residue: 0.1185 time to fit residues: 52.0773 Evaluate side-chains 223 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 0.9980 chunk 112 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 35 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 352 HIS E 432 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.068065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056225 restraints weight = 76856.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057831 restraints weight = 44858.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058939 restraints weight = 30320.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059687 restraints weight = 22695.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060288 restraints weight = 18387.436| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15855 Z= 0.190 Angle : 0.765 16.763 21709 Z= 0.369 Chirality : 0.050 0.851 2698 Planarity : 0.004 0.054 2637 Dihedral : 4.999 27.574 1990 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.13 % Allowed : 0.60 % Favored : 99.27 % 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: -0.19 (0.20), residues: 1656 helix: 0.32 (0.26), residues: 420 sheet: 0.06 (0.24), residues: 416 loop : -0.34 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 588 TYR 0.014 0.002 TYR C 39 PHE 0.027 0.002 PHE E 376 TRP 0.070 0.003 TRP D 596 HIS 0.008 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (15744) covalent geometry : angle 0.70763 / 0.36 (21409) SS BOND : bond 0.00538 / 0.32 ( 33) SS BOND : angle 1.84450 / 1.44 ( 66) hydrogen bonds : bond 0.04716 / 3.14 ( 557) hydrogen bonds : angle 5.12209 / 3.50 ( 1671) link_ALPHA1-3 : bond 0.00427 / 0.21 ( 3) link_ALPHA1-3 : angle 2.29504 / 1.34 ( 9) link_BETA1-4 : bond 0.00247 / 0.16 ( 13) link_BETA1-4 : angle 1.91373 / 1.24 ( 39) link_NAG-ASN : bond 0.00498 / 0.33 ( 62) link_NAG-ASN : angle 2.91582 / 2.02 ( 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 268 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.594 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: A 288 LEU cc_start: 0.9481 (mp) cc_final: 0.9236 (mp) REVERT: A 475 MET cc_start: 0.8908 (mmm) cc_final: 0.7874 (mmm) REVERT: A 490 LYS cc_start: 0.9163 (ttpt) cc_final: 0.8905 (ttpp) REVERT: B 601 LYS cc_start: 0.9273 (pttm) cc_final: 0.9038 (pttm) REVERT: B 634 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 635 ILE cc_start: 0.9553 (tp) cc_final: 0.9036 (tp) REVERT: C 46 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8245 (mmtm) REVERT: C 49 GLU cc_start: 0.8516 (tp30) cc_final: 0.8054 (tp30) REVERT: C 80 ASN cc_start: 0.9012 (t0) cc_final: 0.8723 (t0) REVERT: C 95 MET cc_start: 0.8885 (ppp) cc_final: 0.8020 (ppp) REVERT: C 168 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8872 (mtpt) REVERT: C 271 ILE cc_start: 0.8738 (mt) cc_final: 0.8285 (mt) REVERT: C 316 TRP cc_start: 0.8631 (m100) cc_final: 0.8228 (m100) REVERT: C 390 LEU cc_start: 0.9435 (tp) cc_final: 0.8950 (tp) REVERT: C 484 TYR cc_start: 0.8870 (p90) cc_final: 0.8615 (p90) REVERT: D 577 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 579 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7914 (mtp180) REVERT: D 585 ARG cc_start: 0.9114 (mtp-110) cc_final: 0.8608 (mmm-85) REVERT: D 588 ARG cc_start: 0.8927 (ttp-170) cc_final: 0.8229 (tmm-80) REVERT: E 33 ASN cc_start: 0.8627 (t0) cc_final: 0.8378 (t0) REVERT: E 72 HIS cc_start: 0.8621 (m-70) cc_final: 0.7715 (m-70) REVERT: E 95 MET cc_start: 0.9210 (ppp) cc_final: 0.8731 (ppp) REVERT: E 97 LYS cc_start: 0.9369 (mtpp) cc_final: 0.8974 (mtpp) REVERT: E 100 MET cc_start: 0.9629 (mtm) cc_final: 0.9362 (mtt) REVERT: E 180 ASP cc_start: 0.8525 (m-30) cc_final: 0.8111 (m-30) REVERT: E 381 GLU cc_start: 0.8564 (tp30) cc_final: 0.8329 (tt0) REVERT: F 567 LYS cc_start: 0.9407 (mttt) cc_final: 0.9048 (mmtm) REVERT: F 596 TRP cc_start: 0.8496 (m-10) cc_final: 0.7827 (m-10) REVERT: F 643 TYR cc_start: 0.9347 (m-10) cc_final: 0.8947 (m-80) REVERT: F 651 ASN cc_start: 0.9377 (t0) cc_final: 0.9109 (t0) REVERT: F 653 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8894 (tm-30) REVERT: F 656 ASN cc_start: 0.9119 (m-40) cc_final: 0.8739 (m110) REVERT: F 661 LEU cc_start: 0.8310 (tp) cc_final: 0.8044 (tt) outliers start: 2 outliers final: 1 residues processed: 268 average time/residue: 0.1180 time to fit residues: 47.1284 Evaluate side-chains 213 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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: 10.0000 chunk 167 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 41 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 96 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** 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 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN F 590 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057238 restraints weight = 76440.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.058872 restraints weight = 44571.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.059998 restraints weight = 30261.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060771 restraints weight = 22708.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061376 restraints weight = 18408.759| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15855 Z= 0.134 Angle : 0.716 16.527 21709 Z= 0.345 Chirality : 0.048 0.707 2698 Planarity : 0.004 0.049 2637 Dihedral : 4.839 26.690 1990 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.60 % 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: -0.21 (0.20), residues: 1656 helix: 0.29 (0.26), residues: 429 sheet: 0.03 (0.24), residues: 427 loop : -0.35 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 444 TYR 0.028 0.001 TYR D 586 PHE 0.014 0.001 PHE E 391 TRP 0.072 0.002 TRP D 596 HIS 0.005 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (15744) covalent geometry : angle 0.66195 / 0.33 (21409) SS BOND : bond 0.00483 / 0.29 ( 33) SS BOND : angle 1.60442 / 1.25 ( 66) hydrogen bonds : bond 0.04470 / 2.95 ( 557) hydrogen bonds : angle 4.95132 / 3.37 ( 1671) link_ALPHA1-3 : bond 0.00510 / 0.25 ( 3) link_ALPHA1-3 : angle 2.24383 / 1.29 ( 9) link_BETA1-4 : bond 0.00348 / 0.21 ( 13) link_BETA1-4 : angle 1.72915 / 1.12 ( 39) link_NAG-ASN : bond 0.00449 / 0.26 ( 62) link_NAG-ASN : angle 2.75132 / 1.91 ( 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 273 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.584 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 288 LEU cc_start: 0.9462 (mp) cc_final: 0.9199 (mp) REVERT: A 490 LYS cc_start: 0.9140 (ttpt) cc_final: 0.8882 (ttpp) REVERT: B 595 ILE cc_start: 0.9491 (tp) cc_final: 0.9182 (tp) REVERT: B 634 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 635 ILE cc_start: 0.9553 (tp) cc_final: 0.9006 (tp) REVERT: B 648 GLU cc_start: 0.8966 (pt0) cc_final: 0.8562 (pt0) REVERT: C 46 LYS cc_start: 0.8562 (mmtm) cc_final: 0.8192 (mmtm) REVERT: C 49 GLU cc_start: 0.8495 (tp30) cc_final: 0.8228 (tp30) REVERT: C 80 ASN cc_start: 0.9021 (t0) cc_final: 0.8739 (t0) REVERT: C 95 MET cc_start: 0.8857 (ppp) cc_final: 0.8257 (ppp) REVERT: C 168 LYS cc_start: 0.9241 (mmtt) cc_final: 0.8866 (mtpt) REVERT: C 271 ILE cc_start: 0.8650 (mt) cc_final: 0.8156 (mt) REVERT: C 316 TRP cc_start: 0.8541 (m100) cc_final: 0.8031 (m100) REVERT: C 390 LEU cc_start: 0.9432 (tp) cc_final: 0.8976 (tp) REVERT: C 484 TYR cc_start: 0.8891 (p90) cc_final: 0.8610 (p90) REVERT: D 577 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8609 (tm-30) REVERT: D 579 ARG cc_start: 0.8319 (mtt180) cc_final: 0.7978 (mtp180) REVERT: D 585 ARG cc_start: 0.9114 (mtp-110) cc_final: 0.8727 (mmm-85) REVERT: D 588 ARG cc_start: 0.8894 (ttp-170) cc_final: 0.8166 (tmm-80) REVERT: E 33 ASN cc_start: 0.8622 (t0) cc_final: 0.8350 (t0) REVERT: E 72 HIS cc_start: 0.8571 (m-70) cc_final: 0.7668 (m-70) REVERT: E 95 MET cc_start: 0.9185 (ppp) cc_final: 0.8795 (ppp) REVERT: E 97 LYS cc_start: 0.9373 (mtpp) cc_final: 0.9007 (mtpp) REVERT: E 100 MET cc_start: 0.9635 (mtm) cc_final: 0.9371 (mtt) REVERT: E 180 ASP cc_start: 0.8412 (m-30) cc_final: 0.7921 (m-30) REVERT: F 567 LYS cc_start: 0.9421 (mttt) cc_final: 0.9037 (mmtm) REVERT: F 585 ARG cc_start: 0.8794 (ttm-80) cc_final: 0.8465 (ttm-80) REVERT: F 596 TRP cc_start: 0.8430 (m-10) cc_final: 0.7839 (m-10) REVERT: F 626 MET cc_start: 0.8248 (tmm) cc_final: 0.7628 (tmm) REVERT: F 656 ASN cc_start: 0.9067 (m-40) cc_final: 0.8866 (m-40) REVERT: F 661 LEU cc_start: 0.8206 (tp) cc_final: 0.7936 (tt) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.1286 time to fit residues: 52.2326 Evaluate side-chains 218 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 0.0980 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 0.0070 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** 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 = 0.3274 r_free = 0.3274 target = 0.069692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.057526 restraints weight = 77245.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.059141 restraints weight = 45311.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060251 restraints weight = 30926.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061079 restraints weight = 23367.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.061507 restraints weight = 18855.838| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15855 Z= 0.130 Angle : 0.697 16.130 21709 Z= 0.337 Chirality : 0.048 0.601 2698 Planarity : 0.004 0.052 2637 Dihedral : 4.781 26.120 1990 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.72 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: -0.19 (0.20), residues: 1656 helix: 0.35 (0.26), residues: 426 sheet: 0.02 (0.24), residues: 428 loop : -0.35 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 588 TYR 0.055 0.002 TYR F 643 PHE 0.016 0.001 PHE A 53 TRP 0.073 0.002 TRP D 596 HIS 0.009 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15744) covalent geometry : angle 0.64507 / 0.33 (21409) SS BOND : bond 0.00540 / 0.34 ( 33) SS BOND : angle 1.54660 / 1.17 ( 66) hydrogen bonds : bond 0.04315 / 2.84 ( 557) hydrogen bonds : angle 4.85956 / 3.33 ( 1671) link_ALPHA1-3 : bond 0.00512 / 0.25 ( 3) link_ALPHA1-3 : angle 2.17871 / 1.25 ( 9) link_BETA1-4 : bond 0.00333 / 0.20 ( 13) link_BETA1-4 : angle 1.68189 / 1.08 ( 39) link_NAG-ASN : bond 0.00449 / 0.27 ( 62) link_NAG-ASN : angle 2.65705 / 1.85 ( 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 274 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.635 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: A 288 LEU cc_start: 0.9466 (mp) cc_final: 0.9218 (mp) REVERT: A 490 LYS cc_start: 0.9144 (ttpt) cc_final: 0.8911 (ttpp) REVERT: B 596 TRP cc_start: 0.8863 (m-10) cc_final: 0.8494 (m-10) REVERT: B 634 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 635 ILE cc_start: 0.9525 (tp) cc_final: 0.8986 (tp) REVERT: B 645 LEU cc_start: 0.9536 (mt) cc_final: 0.9301 (mt) REVERT: B 646 LEU cc_start: 0.9436 (mt) cc_final: 0.9081 (mt) REVERT: B 656 ASN cc_start: 0.8901 (m110) cc_final: 0.8686 (m110) REVERT: C 46 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8142 (mmtm) REVERT: C 49 GLU cc_start: 0.8546 (tp30) cc_final: 0.8053 (tp30) REVERT: C 80 ASN cc_start: 0.8949 (t0) cc_final: 0.8683 (t0) REVERT: C 95 MET cc_start: 0.8811 (ppp) cc_final: 0.8325 (ppp) REVERT: C 103 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8544 (tp40) REVERT: C 168 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8784 (mtpt) REVERT: C 271 ILE cc_start: 0.8648 (mt) cc_final: 0.8075 (mt) REVERT: C 316 TRP cc_start: 0.8512 (m100) cc_final: 0.7989 (m100) REVERT: C 390 LEU cc_start: 0.9428 (tp) cc_final: 0.8988 (tp) REVERT: C 484 TYR cc_start: 0.8891 (p90) cc_final: 0.8596 (p90) REVERT: C 492 GLU cc_start: 0.8043 (mp0) cc_final: 0.6944 (mp0) REVERT: D 577 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8613 (tm-30) REVERT: D 579 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7968 (mtp180) REVERT: D 585 ARG cc_start: 0.9067 (mtp-110) cc_final: 0.8670 (mmm-85) REVERT: D 588 ARG cc_start: 0.8851 (ttp-170) cc_final: 0.8196 (tmm-80) REVERT: E 33 ASN cc_start: 0.8615 (t0) cc_final: 0.8363 (t0) REVERT: E 72 HIS cc_start: 0.8535 (m-70) cc_final: 0.7985 (m-70) REVERT: E 95 MET cc_start: 0.9173 (ppp) cc_final: 0.8833 (ppp) REVERT: E 97 LYS cc_start: 0.9344 (mtpp) cc_final: 0.9006 (mtpp) REVERT: E 180 ASP cc_start: 0.8342 (m-30) cc_final: 0.7813 (m-30) REVERT: F 567 LYS cc_start: 0.9406 (mttt) cc_final: 0.9038 (mmtm) REVERT: F 585 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8425 (ttm-80) REVERT: F 596 TRP cc_start: 0.8675 (m-10) cc_final: 0.8296 (m-10) REVERT: F 626 MET cc_start: 0.8237 (tmm) cc_final: 0.7592 (tmm) REVERT: F 661 LEU cc_start: 0.8109 (tp) cc_final: 0.7852 (tt) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.1257 time to fit residues: 51.6429 Evaluate side-chains 215 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 3.9990 chunk 170 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 159 optimal weight: 0.1980 chunk 174 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN A 300 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 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 607 ASN ** 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 = 0.3255 r_free = 0.3255 target = 0.068982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.056967 restraints weight = 77293.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058552 restraints weight = 45849.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059637 restraints weight = 31328.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060395 restraints weight = 23779.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060989 restraints weight = 19413.481| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15855 Z= 0.153 Angle : 0.702 15.706 21709 Z= 0.342 Chirality : 0.047 0.551 2698 Planarity : 0.004 0.051 2637 Dihedral : 4.767 27.081 1990 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.24 (0.20), residues: 1656 helix: 0.27 (0.26), residues: 427 sheet: 0.04 (0.24), residues: 426 loop : -0.38 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 588 TYR 0.045 0.002 TYR F 643 PHE 0.014 0.001 PHE E 391 TRP 0.072 0.003 TRP D 596 HIS 0.011 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (15744) covalent geometry : angle 0.65302 / 0.33 (21409) SS BOND : bond 0.00486 / 0.29 ( 33) SS BOND : angle 1.47499 / 1.11 ( 66) hydrogen bonds : bond 0.04349 / 2.87 ( 557) hydrogen bonds : angle 4.85973 / 3.32 ( 1671) link_ALPHA1-3 : bond 0.00443 / 0.22 ( 3) link_ALPHA1-3 : angle 2.20136 / 1.27 ( 9) link_BETA1-4 : bond 0.00274 / 0.17 ( 13) link_BETA1-4 : angle 1.76248 / 1.15 ( 39) link_NAG-ASN : bond 0.00441 / 0.28 ( 62) link_NAG-ASN : angle 2.61624 / 1.82 ( 186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.10 seconds wall clock time: 39 minutes 57.99 seconds (2397.99 seconds total)