Starting phenix.real_space_refine on Sat Aug 23 23:12:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f9g_28942/08_2025/8f9g_28942.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f9g_28942/08_2025/8f9g_28942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f9g_28942/08_2025/8f9g_28942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f9g_28942/08_2025/8f9g_28942.map" model { file = "/net/cci-nas-00/data/ceres_data/8f9g_28942/08_2025/8f9g_28942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f9g_28942/08_2025/8f9g_28942.cif" } resolution = 3.2 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= 0.054 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 105 5.16 5 C 9496 2.51 5 N 2575 2.21 5 O 2978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15154 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3428 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 23, 'TRANS': 408} Chain breaks: 4 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 944 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3428 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 23, 'TRANS': 408} Chain breaks: 4 Chain: "G" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 920 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "F" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3428 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 23, 'TRANS': 408} Chain breaks: 4 Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 932 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "H" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 640 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'TRANS': 127} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 128 Planarities with less than four sites: {'UNK:plan-1': 128} Unresolved non-hydrogen planarities: 128 Chain: "L" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 520 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'TRANS': 103} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'UNK:plan-1': 104} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.08, per 1000 atoms: 0.27 Number of scatterers: 15154 At special positions: 0 Unit cell: (123.431, 139.461, 145.873, 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 105 16.00 O 2978 8.00 N 2575 7.00 C 9496 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 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.04 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA K 3 " - " MAN K 4 " " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 386 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 276 " " NAG B 701 " - " ASN B 611 " " NAG C 1 " - " ASN A 332 " " NAG D 1 " - " ASN A 156 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 355 " " NAG E 608 " - " ASN E 386 " " NAG E 609 " - " ASN E 392 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 197 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 234 " " NAG F 604 " - " ASN F 295 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 339 " " NAG F 607 " - " ASN F 355 " " NAG F 608 " - " ASN F 386 " " NAG F 609 " - " ASN F 392 " " NAG F 610 " - " ASN F 448 " " NAG G 701 " - " ASN G 611 " " NAG I 701 " - " ASN I 611 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN E 156 " " NAG N 1 " - " ASN E 262 " " NAG O 1 " - " ASN E 276 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN F 156 " " NAG R 1 " - " ASN F 197 " " NAG S 1 " - " ASN F 262 " " NAG T 1 " - " ASN F 276 " " NAG U 1 " - " ASN F 332 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 699.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 31 sheets defined 29.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.172A 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 335 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.334A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 545 removed outlier: 3.672A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.366A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.836A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.169A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.945A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.459A pdb=" N GLY G 527 " --> pdb=" O GLY G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 535 removed outlier: 3.751A pdb=" N MET G 535 " --> pdb=" O GLY G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 544 removed outlier: 4.239A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 662 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.146A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.588A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.927A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.651A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.650A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 596 Processing helix chain 'I' and resid 619 through 626 removed outlier: 3.507A pdb=" N TRP I 623 " --> pdb=" O LEU I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 663 removed outlier: 3.672A pdb=" N GLY I 644 " --> pdb=" O GLN I 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'L' and resid 23 through 27 removed outlier: 4.227A pdb=" N UNK L 26 " --> pdb=" O UNK L 23 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.930A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (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 53 through 55 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 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.534A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 7.117A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.281A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AB5, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AB6, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.686A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 7.119A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB9, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.493A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AC5, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.631A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 256 through 257 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 256 through 257 current: chain 'F' and resid 284 through 308 removed outlier: 6.924A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 316 through 323A current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 470 Processing sheet with id=AC8, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AC9, first strand: chain 'H' and resid 50 through 52 removed outlier: 7.054A pdb=" N UNK H 96 " --> pdb=" O UNK H 119 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N UNK H 119 " --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N UNK H 98 " --> pdb=" O UNK H 117 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N UNK H 117 " --> pdb=" O UNK H 98 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N UNK H 100 " --> pdb=" O UNK H 115 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 8 through 9 removed outlier: 6.474A pdb=" N UNK L 8 " --> pdb=" O UNK L 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 21 Processing sheet with id=AD3, first strand: chain 'L' and resid 42 through 43 Processing sheet with id=AD4, first strand: chain 'L' and resid 45 through 46 468 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4798 1.34 - 1.46: 3743 1.46 - 1.59: 6746 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 15431 Sorted by residual: bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" N CYS A 54 " pdb=" CA CYS A 54 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N PHE A 53 " pdb=" CA PHE A 53 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.83e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.44e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.83e+00 ... (remaining 15426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 19739 2.01 - 4.01: 1084 4.01 - 6.02: 136 6.02 - 8.03: 17 8.03 - 10.04: 5 Bond angle restraints: 20981 Sorted by residual: angle pdb=" N CYS E 157 " pdb=" CA CYS E 157 " pdb=" C CYS E 157 " ideal model delta sigma weight residual 111.24 117.64 -6.40 1.38e+00 5.25e-01 2.15e+01 angle pdb=" N CYS F 196 " pdb=" CA CYS F 196 " pdb=" C CYS F 196 " ideal model delta sigma weight residual 111.71 115.79 -4.08 1.15e+00 7.56e-01 1.26e+01 angle pdb=" C LYS F 155 " pdb=" N ASN F 156 " pdb=" CA ASN F 156 " ideal model delta sigma weight residual 122.41 127.55 -5.14 1.47e+00 4.63e-01 1.22e+01 angle pdb=" N SER F 199 " pdb=" CA SER F 199 " pdb=" C SER F 199 " ideal model delta sigma weight residual 108.79 114.13 -5.34 1.53e+00 4.27e-01 1.22e+01 angle pdb=" CB ASN F 156 " pdb=" CG ASN F 156 " pdb=" ND2 ASN F 156 " ideal model delta sigma weight residual 116.40 111.22 5.18 1.50e+00 4.44e-01 1.19e+01 ... (remaining 20976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.60: 9799 21.60 - 43.19: 259 43.19 - 64.79: 57 64.79 - 86.38: 34 86.38 - 107.98: 24 Dihedral angle restraints: 10173 sinusoidal: 4710 harmonic: 5463 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.49 -54.49 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 146.93 -53.93 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 145.87 -52.87 1 1.00e+01 1.00e-02 3.80e+01 ... (remaining 10170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 2599 0.302 - 0.604: 3 0.604 - 0.905: 0 0.905 - 1.207: 0 1.207 - 1.509: 1 Chirality restraints: 2603 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN F 156 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.69e+01 chirality pdb=" C5 BMA S 3 " pdb=" C4 BMA S 3 " pdb=" C6 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2600 not shown) Planarity restraints: 2639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 647 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C GLU B 647 " -0.075 2.00e-02 2.50e+03 pdb=" O GLU B 647 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU B 648 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ARG A 476 " -0.074 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.028 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 646 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C LEU G 646 " 0.073 2.00e-02 2.50e+03 pdb=" O LEU G 646 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU G 647 " -0.024 2.00e-02 2.50e+03 ... (remaining 2636 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1216 2.74 - 3.28: 14635 3.28 - 3.82: 23931 3.82 - 4.36: 29137 4.36 - 4.90: 48595 Nonbonded interactions: 117514 Sorted by model distance: nonbonded pdb=" OD1 ASP F 107 " pdb=" NZ LYS I 574 " model vdw 2.197 3.120 nonbonded pdb=" O ASN A 80 " pdb=" NE2 GLN A 82 " model vdw 2.251 3.120 nonbonded pdb=" O4 BMA K 3 " pdb=" O6 BMA K 3 " model vdw 2.265 3.040 nonbonded pdb=" O3 NAG M 1 " pdb=" O5 NAG M 2 " model vdw 2.320 3.040 nonbonded pdb=" O4 BMA S 3 " pdb=" O6 BMA S 3 " model vdw 2.329 3.040 ... (remaining 117509 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' selection = (chain 'E' and resid 33 through 609) selection = (chain 'F' and resid 33 through 609) } ncs_group { reference = (chain 'B' and (resid 521 through 545 or resid 573 through 662 or resid 701)) selection = (chain 'G' and (resid 521 through 545 or resid 573 through 701)) selection = (chain 'I' and (resid 521 through 662 or resid 701)) } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.090 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.010 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.006 0.068 15531 Z= 0.302 Angle : 1.092 20.696 21248 Z= 0.578 Chirality : 0.066 1.509 2603 Planarity : 0.007 0.043 2593 Dihedral : 12.571 107.980 6516 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.14 % Allowed : 0.34 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.20), residues: 1606 helix: 0.73 (0.24), residues: 431 sheet: 1.48 (0.26), residues: 357 loop : 0.59 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 542 TYR 0.021 0.003 TYR F 191 PHE 0.032 0.003 PHE E 383 TRP 0.028 0.003 TRP F 479 HIS 0.007 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00639 (15431) covalent geometry : angle 1.03608 (20981) SS BOND : bond 0.00467 ( 33) SS BOND : angle 2.47109 ( 66) hydrogen bonds : bond 0.15388 ( 468) hydrogen bonds : angle 7.41081 ( 1272) link_ALPHA1-3 : bond 0.00489 ( 4) link_ALPHA1-3 : angle 2.18651 ( 12) link_BETA1-4 : bond 0.00859 ( 17) link_BETA1-4 : angle 3.37027 ( 51) link_NAG-ASN : bond 0.00290 ( 46) link_NAG-ASN : angle 3.56351 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6679 (mm-30) REVERT: A 209 SER cc_start: 0.8263 (t) cc_final: 0.7969 (p) REVERT: A 340 GLU cc_start: 0.8424 (tt0) cc_final: 0.7863 (tp30) REVERT: A 370 GLU cc_start: 0.7401 (tt0) cc_final: 0.7056 (mt-10) REVERT: A 427 TRP cc_start: 0.7943 (m-90) cc_final: 0.7691 (m-90) REVERT: A 502 LYS cc_start: 0.8537 (mttt) cc_final: 0.7699 (tttm) REVERT: B 522 PHE cc_start: 0.7956 (t80) cc_final: 0.7564 (t80) REVERT: B 536 THR cc_start: 0.8062 (p) cc_final: 0.7663 (t) REVERT: B 538 THR cc_start: 0.7880 (m) cc_final: 0.7543 (m) REVERT: E 84 ILE cc_start: 0.7231 (mm) cc_final: 0.7018 (mp) REVERT: E 103 GLN cc_start: 0.6913 (tt0) cc_final: 0.6602 (tm-30) REVERT: E 154 ILE cc_start: 0.8378 (mt) cc_final: 0.7991 (mt) REVERT: E 199 SER cc_start: 0.8886 (p) cc_final: 0.8067 (m) REVERT: E 232 LYS cc_start: 0.7459 (mttt) cc_final: 0.6936 (tptt) REVERT: E 502 LYS cc_start: 0.8525 (pttm) cc_final: 0.8073 (tmtt) REVERT: G 636 SER cc_start: 0.9121 (t) cc_final: 0.8677 (m) REVERT: G 645 LEU cc_start: 0.9033 (mt) cc_final: 0.8338 (mt) REVERT: F 84 ILE cc_start: 0.7634 (mm) cc_final: 0.7431 (mp) REVERT: F 158 SER cc_start: 0.8460 (t) cc_final: 0.8193 (p) REVERT: F 211 GLU cc_start: 0.8782 (tt0) cc_final: 0.8515 (pt0) REVERT: F 232 LYS cc_start: 0.7799 (mttt) cc_final: 0.6925 (mtmm) REVERT: F 283 ASN cc_start: 0.8534 (m-40) cc_final: 0.8109 (m-40) REVERT: F 327 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7024 (mtp85) REVERT: F 368 ASP cc_start: 0.7943 (m-30) cc_final: 0.7451 (p0) REVERT: I 536 THR cc_start: 0.7020 (p) cc_final: 0.6665 (p) REVERT: I 539 VAL cc_start: 0.7947 (t) cc_final: 0.7629 (t) REVERT: I 540 GLN cc_start: 0.6974 (mp-120) cc_final: 0.6702 (mp10) REVERT: I 543 ASN cc_start: 0.7102 (m-40) cc_final: 0.6531 (m-40) REVERT: I 545 LEU cc_start: 0.6556 (mt) cc_final: 0.5888 (mt) REVERT: I 601 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7719 (mtpp) REVERT: I 607 ASN cc_start: 0.8382 (m-40) cc_final: 0.7834 (m-40) REVERT: I 624 ASP cc_start: 0.8265 (m-30) cc_final: 0.7782 (m-30) REVERT: I 625 ASN cc_start: 0.8630 (m-40) cc_final: 0.8405 (t0) REVERT: I 635 ILE cc_start: 0.8521 (pt) cc_final: 0.8260 (pt) REVERT: I 636 SER cc_start: 0.8095 (t) cc_final: 0.7717 (m) outliers start: 2 outliers final: 1 residues processed: 391 average time/residue: 0.1405 time to fit residues: 78.9539 Evaluate side-chains 224 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN E 348 GLN G 616 ASN ** F 374 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.144289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.111731 restraints weight = 25208.736| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.14 r_work: 0.3397 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15531 Z= 0.162 Angle : 0.711 17.487 21248 Z= 0.340 Chirality : 0.044 0.410 2603 Planarity : 0.004 0.044 2593 Dihedral : 8.703 65.252 3369 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 7.23 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.21), residues: 1606 helix: 1.43 (0.25), residues: 452 sheet: 0.97 (0.25), residues: 411 loop : 0.32 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 503 TYR 0.014 0.001 TYR A 217 PHE 0.023 0.002 PHE F 53 TRP 0.020 0.002 TRP E 479 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00366 (15431) covalent geometry : angle 0.65517 (20981) SS BOND : bond 0.00496 ( 33) SS BOND : angle 1.42233 ( 66) hydrogen bonds : bond 0.05595 ( 468) hydrogen bonds : angle 5.16944 ( 1272) link_ALPHA1-3 : bond 0.01008 ( 4) link_ALPHA1-3 : angle 2.78456 ( 12) link_BETA1-4 : bond 0.01033 ( 17) link_BETA1-4 : angle 3.10521 ( 51) link_NAG-ASN : bond 0.00296 ( 46) link_NAG-ASN : angle 2.71160 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7428 (mm-30) REVERT: A 107 ASP cc_start: 0.8524 (m-30) cc_final: 0.8314 (m-30) REVERT: A 268 GLU cc_start: 0.7407 (tp30) cc_final: 0.7060 (mt-10) REVERT: A 340 GLU cc_start: 0.8418 (tt0) cc_final: 0.8003 (tp30) REVERT: A 475 MET cc_start: 0.8146 (mmm) cc_final: 0.7284 (mmm) REVERT: B 522 PHE cc_start: 0.8134 (t80) cc_final: 0.7623 (t80) REVERT: B 543 ASN cc_start: 0.8016 (m-40) cc_final: 0.7307 (m-40) REVERT: B 625 ASN cc_start: 0.8595 (t0) cc_final: 0.8386 (t0) REVERT: E 103 GLN cc_start: 0.7941 (tt0) cc_final: 0.7592 (tm-30) REVERT: E 154 ILE cc_start: 0.8967 (mt) cc_final: 0.8682 (mt) REVERT: E 199 SER cc_start: 0.9302 (p) cc_final: 0.8812 (m) REVERT: E 232 LYS cc_start: 0.7755 (mttt) cc_final: 0.7133 (tptt) REVERT: E 280 ASN cc_start: 0.8510 (m-40) cc_final: 0.8253 (m-40) REVERT: E 502 LYS cc_start: 0.8468 (pttm) cc_final: 0.8177 (tmtt) REVERT: G 590 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: G 636 SER cc_start: 0.9109 (t) cc_final: 0.8680 (m) REVERT: F 49 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7451 (pm20) REVERT: F 66 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.5504 (t-90) REVERT: F 211 GLU cc_start: 0.8994 (tt0) cc_final: 0.8602 (pt0) REVERT: F 327 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7512 (mtp85) REVERT: F 368 ASP cc_start: 0.8025 (m-30) cc_final: 0.7544 (p0) REVERT: F 426 MET cc_start: 0.8124 (mtp) cc_final: 0.7873 (mtp) REVERT: I 539 VAL cc_start: 0.8494 (t) cc_final: 0.8002 (t) REVERT: I 543 ASN cc_start: 0.7926 (m-40) cc_final: 0.7460 (m110) REVERT: I 607 ASN cc_start: 0.8430 (m-40) cc_final: 0.7969 (m-40) REVERT: I 624 ASP cc_start: 0.8295 (m-30) cc_final: 0.7836 (m-30) REVERT: I 625 ASN cc_start: 0.8639 (m-40) cc_final: 0.8358 (t0) REVERT: I 636 SER cc_start: 0.8368 (t) cc_final: 0.8158 (m) REVERT: I 648 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8245 (pt0) REVERT: I 658 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7707 (tm-30) outliers start: 28 outliers final: 13 residues processed: 256 average time/residue: 0.1025 time to fit residues: 39.3278 Evaluate side-chains 217 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 649 SER Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN E 85 HIS E 195 ASN E 249 HIS G 616 ASN ** F 374 HIS ** 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 = 0.3930 r_free = 0.3930 target = 0.142365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109719 restraints weight = 25241.341| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.15 r_work: 0.3384 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15531 Z= 0.141 Angle : 0.635 17.398 21248 Z= 0.305 Chirality : 0.043 0.400 2603 Planarity : 0.003 0.037 2593 Dihedral : 6.966 53.522 3368 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.59 % Allowed : 8.39 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.21), residues: 1606 helix: 1.41 (0.26), residues: 454 sheet: 1.10 (0.24), residues: 453 loop : -0.01 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 617 TYR 0.011 0.001 TYR E 39 PHE 0.018 0.002 PHE E 320 TRP 0.015 0.001 TRP E 479 HIS 0.004 0.001 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00320 (15431) covalent geometry : angle 0.58836 (20981) SS BOND : bond 0.00443 ( 33) SS BOND : angle 1.36538 ( 66) hydrogen bonds : bond 0.04645 ( 468) hydrogen bonds : angle 4.73904 ( 1272) link_ALPHA1-3 : bond 0.01169 ( 4) link_ALPHA1-3 : angle 1.67298 ( 12) link_BETA1-4 : bond 0.01002 ( 17) link_BETA1-4 : angle 2.89470 ( 51) link_NAG-ASN : bond 0.00202 ( 46) link_NAG-ASN : angle 2.29550 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.444 Fit side-chains REVERT: A 107 ASP cc_start: 0.8475 (m-30) cc_final: 0.8210 (m-30) REVERT: A 231 LYS cc_start: 0.8007 (mttt) cc_final: 0.7770 (mttm) REVERT: A 268 GLU cc_start: 0.7477 (tp30) cc_final: 0.7039 (mt-10) REVERT: A 475 MET cc_start: 0.8118 (mmm) cc_final: 0.7235 (mmm) REVERT: A 503 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.5963 (tpt170) REVERT: B 522 PHE cc_start: 0.8146 (t80) cc_final: 0.7612 (t80) REVERT: B 543 ASN cc_start: 0.7983 (m-40) cc_final: 0.7258 (m-40) REVERT: B 544 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8010 (mm) REVERT: B 591 GLN cc_start: 0.8135 (tt0) cc_final: 0.7610 (tp40) REVERT: E 51 THR cc_start: 0.8939 (m) cc_final: 0.8426 (p) REVERT: E 103 GLN cc_start: 0.7894 (tt0) cc_final: 0.7529 (tm-30) REVERT: E 199 SER cc_start: 0.9342 (p) cc_final: 0.8649 (m) REVERT: E 232 LYS cc_start: 0.7837 (mttt) cc_final: 0.7143 (tptt) REVERT: E 280 ASN cc_start: 0.8545 (m-40) cc_final: 0.8270 (m-40) REVERT: G 590 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: F 66 HIS cc_start: 0.6084 (OUTLIER) cc_final: 0.5536 (t-90) REVERT: F 161 MET cc_start: 0.8537 (tpt) cc_final: 0.8143 (tpt) REVERT: F 211 GLU cc_start: 0.9017 (tt0) cc_final: 0.8611 (pt0) REVERT: F 368 ASP cc_start: 0.8028 (m-30) cc_final: 0.7576 (p0) REVERT: I 539 VAL cc_start: 0.8388 (t) cc_final: 0.7898 (t) REVERT: I 543 ASN cc_start: 0.7900 (m-40) cc_final: 0.7435 (m110) REVERT: I 607 ASN cc_start: 0.8549 (m-40) cc_final: 0.8067 (m-40) REVERT: I 624 ASP cc_start: 0.8340 (m-30) cc_final: 0.7881 (m-30) REVERT: I 625 ASN cc_start: 0.8651 (m-40) cc_final: 0.8254 (t0) REVERT: I 648 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8183 (pt0) outliers start: 38 outliers final: 19 residues processed: 246 average time/residue: 0.1180 time to fit residues: 42.6030 Evaluate side-chains 225 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.138872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105975 restraints weight = 25397.170| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.13 r_work: 0.3325 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15531 Z= 0.190 Angle : 0.672 17.082 21248 Z= 0.323 Chirality : 0.044 0.401 2603 Planarity : 0.003 0.039 2593 Dihedral : 6.464 56.656 3368 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.80 % Allowed : 8.59 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.21), residues: 1606 helix: 1.62 (0.27), residues: 430 sheet: 1.25 (0.24), residues: 423 loop : -0.30 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 617 TYR 0.011 0.001 TYR E 217 PHE 0.017 0.002 PHE E 320 TRP 0.016 0.002 TRP I 631 HIS 0.005 0.001 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00449 (15431) covalent geometry : angle 0.62859 (20981) SS BOND : bond 0.00417 ( 33) SS BOND : angle 1.54649 ( 66) hydrogen bonds : bond 0.04592 ( 468) hydrogen bonds : angle 4.69683 ( 1272) link_ALPHA1-3 : bond 0.01129 ( 4) link_ALPHA1-3 : angle 1.87375 ( 12) link_BETA1-4 : bond 0.00834 ( 17) link_BETA1-4 : angle 2.94313 ( 51) link_NAG-ASN : bond 0.00192 ( 46) link_NAG-ASN : angle 2.21045 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7444 (tt0) REVERT: A 107 ASP cc_start: 0.8418 (m-30) cc_final: 0.8172 (m-30) REVERT: A 268 GLU cc_start: 0.7442 (tp30) cc_final: 0.6962 (tt0) REVERT: A 425 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7836 (t0) REVERT: A 502 LYS cc_start: 0.8689 (mttt) cc_final: 0.8151 (ttmt) REVERT: A 503 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.5881 (tpp-160) REVERT: B 522 PHE cc_start: 0.8208 (t80) cc_final: 0.7515 (t80) REVERT: B 543 ASN cc_start: 0.8021 (m-40) cc_final: 0.7195 (m-40) REVERT: E 51 THR cc_start: 0.8970 (m) cc_final: 0.8493 (p) REVERT: E 53 PHE cc_start: 0.7580 (m-80) cc_final: 0.7279 (m-10) REVERT: E 103 GLN cc_start: 0.7931 (tt0) cc_final: 0.7544 (tm-30) REVERT: E 232 LYS cc_start: 0.8030 (mttt) cc_final: 0.7185 (tptt) REVERT: E 280 ASN cc_start: 0.8618 (m-40) cc_final: 0.8320 (m-40) REVERT: G 535 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8495 (ttm) REVERT: G 590 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: G 616 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6193 (m-40) REVERT: G 648 GLU cc_start: 0.8373 (tp30) cc_final: 0.8070 (tp30) REVERT: G 653 GLN cc_start: 0.6817 (mt0) cc_final: 0.6598 (mt0) REVERT: F 49 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7514 (pm20) REVERT: F 66 HIS cc_start: 0.6038 (OUTLIER) cc_final: 0.5479 (t-90) REVERT: F 151 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7808 (ttm170) REVERT: F 161 MET cc_start: 0.8599 (tpt) cc_final: 0.8281 (tpt) REVERT: F 211 GLU cc_start: 0.9062 (tt0) cc_final: 0.8635 (pt0) REVERT: F 368 ASP cc_start: 0.8029 (m-30) cc_final: 0.7593 (p0) REVERT: I 539 VAL cc_start: 0.8302 (t) cc_final: 0.7849 (t) REVERT: I 543 ASN cc_start: 0.7945 (m-40) cc_final: 0.7470 (m110) REVERT: I 607 ASN cc_start: 0.8576 (m-40) cc_final: 0.8283 (m-40) REVERT: I 617 ARG cc_start: 0.7700 (ptm-80) cc_final: 0.7413 (ptm-80) REVERT: I 626 MET cc_start: 0.7525 (mtt) cc_final: 0.7235 (mtt) REVERT: I 648 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8134 (pt0) outliers start: 41 outliers final: 22 residues processed: 224 average time/residue: 0.1022 time to fit residues: 33.8699 Evaluate side-chains 223 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 587 LEU Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN B 653 GLN E 195 ASN E 289 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 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 = 0.3889 r_free = 0.3889 target = 0.139089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106288 restraints weight = 25304.569| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.13 r_work: 0.3324 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15531 Z= 0.165 Angle : 0.644 17.398 21248 Z= 0.308 Chirality : 0.043 0.399 2603 Planarity : 0.003 0.050 2593 Dihedral : 6.202 58.253 3368 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.39 % Allowed : 9.55 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.21), residues: 1606 helix: 1.51 (0.26), residues: 436 sheet: 1.18 (0.25), residues: 423 loop : -0.45 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 617 TYR 0.010 0.001 TYR E 40 PHE 0.013 0.002 PHE E 320 TRP 0.027 0.001 TRP I 631 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00386 (15431) covalent geometry : angle 0.59831 (20981) SS BOND : bond 0.00371 ( 33) SS BOND : angle 1.78845 ( 66) hydrogen bonds : bond 0.04409 ( 468) hydrogen bonds : angle 4.63493 ( 1272) link_ALPHA1-3 : bond 0.01217 ( 4) link_ALPHA1-3 : angle 1.74665 ( 12) link_BETA1-4 : bond 0.00955 ( 17) link_BETA1-4 : angle 2.93479 ( 51) link_NAG-ASN : bond 0.00158 ( 46) link_NAG-ASN : angle 2.11999 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7429 (tt0) REVERT: A 268 GLU cc_start: 0.7562 (tp30) cc_final: 0.7017 (tt0) REVERT: A 349 LEU cc_start: 0.8441 (mp) cc_final: 0.8188 (mp) REVERT: A 475 MET cc_start: 0.8171 (mmm) cc_final: 0.7307 (mmm) REVERT: A 502 LYS cc_start: 0.8699 (mttt) cc_final: 0.8157 (ttmt) REVERT: A 503 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.5806 (tpp-160) REVERT: B 522 PHE cc_start: 0.8202 (t80) cc_final: 0.7515 (t80) REVERT: B 544 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8167 (mm) REVERT: B 591 GLN cc_start: 0.8163 (tt0) cc_final: 0.7630 (tp40) REVERT: E 51 THR cc_start: 0.9014 (m) cc_final: 0.8524 (p) REVERT: E 103 GLN cc_start: 0.7917 (tt0) cc_final: 0.7533 (tm-30) REVERT: E 199 SER cc_start: 0.9317 (p) cc_final: 0.8917 (m) REVERT: E 232 LYS cc_start: 0.8066 (mttt) cc_final: 0.7247 (tptt) REVERT: E 280 ASN cc_start: 0.8618 (m-40) cc_final: 0.8310 (m-40) REVERT: G 590 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6771 (mp10) REVERT: G 648 GLU cc_start: 0.8374 (tp30) cc_final: 0.8076 (tp30) REVERT: G 653 GLN cc_start: 0.6842 (mt0) cc_final: 0.6638 (mt0) REVERT: F 66 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.5530 (t-90) REVERT: F 151 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7810 (ttm170) REVERT: F 161 MET cc_start: 0.8603 (tpt) cc_final: 0.8348 (tpt) REVERT: F 211 GLU cc_start: 0.9046 (tt0) cc_final: 0.8648 (pt0) REVERT: F 368 ASP cc_start: 0.8053 (m-30) cc_final: 0.7600 (p0) REVERT: I 543 ASN cc_start: 0.7890 (m-40) cc_final: 0.7427 (m-40) REVERT: I 601 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8111 (mtpp) REVERT: I 607 ASN cc_start: 0.8559 (m-40) cc_final: 0.8323 (m-40) REVERT: I 617 ARG cc_start: 0.7577 (ptm-80) cc_final: 0.7242 (ptm-80) REVERT: I 648 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8118 (pt0) outliers start: 35 outliers final: 25 residues processed: 225 average time/residue: 0.1297 time to fit residues: 42.8866 Evaluate side-chains 224 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 587 LEU Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 26 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 180 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 HIS B 653 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN F 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102208 restraints weight = 25555.137| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.06 r_work: 0.3275 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 15531 Z= 0.274 Angle : 0.743 17.588 21248 Z= 0.356 Chirality : 0.047 0.416 2603 Planarity : 0.004 0.048 2593 Dihedral : 6.531 56.750 3368 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.66 % Allowed : 9.28 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.21), residues: 1606 helix: 1.56 (0.27), residues: 412 sheet: 0.82 (0.25), residues: 423 loop : -0.66 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 617 TYR 0.018 0.002 TYR E 217 PHE 0.016 0.002 PHE A 317 TRP 0.034 0.002 TRP I 631 HIS 0.007 0.002 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00656 (15431) covalent geometry : angle 0.69780 (20981) SS BOND : bond 0.00563 ( 33) SS BOND : angle 1.78305 ( 66) hydrogen bonds : bond 0.05038 ( 468) hydrogen bonds : angle 4.92362 ( 1272) link_ALPHA1-3 : bond 0.01247 ( 4) link_ALPHA1-3 : angle 1.83987 ( 12) link_BETA1-4 : bond 0.00864 ( 17) link_BETA1-4 : angle 3.14292 ( 51) link_NAG-ASN : bond 0.00316 ( 46) link_NAG-ASN : angle 2.36261 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8964 (t0) cc_final: 0.8663 (t0) REVERT: A 107 ASP cc_start: 0.8378 (m-30) cc_final: 0.8141 (m-30) REVERT: A 268 GLU cc_start: 0.7559 (tp30) cc_final: 0.7023 (tt0) REVERT: A 425 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7889 (t0) REVERT: A 502 LYS cc_start: 0.8807 (mttt) cc_final: 0.8351 (ttmt) REVERT: A 503 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.5892 (tpp-160) REVERT: B 522 PHE cc_start: 0.8213 (t80) cc_final: 0.7544 (t80) REVERT: B 544 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8405 (mm) REVERT: E 51 THR cc_start: 0.9108 (m) cc_final: 0.8690 (p) REVERT: E 103 GLN cc_start: 0.8019 (tt0) cc_final: 0.7615 (tm-30) REVERT: E 232 LYS cc_start: 0.8206 (mttt) cc_final: 0.7343 (tptt) REVERT: E 325 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7207 (t-90) REVERT: G 590 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: G 616 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.6575 (m110) REVERT: G 648 GLU cc_start: 0.8448 (tp30) cc_final: 0.8158 (tp30) REVERT: F 49 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7655 (pm20) REVERT: F 66 HIS cc_start: 0.6221 (OUTLIER) cc_final: 0.5677 (t-90) REVERT: F 151 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: F 161 MET cc_start: 0.8682 (tpt) cc_final: 0.8343 (tpt) REVERT: F 211 GLU cc_start: 0.9099 (tt0) cc_final: 0.8698 (pt0) REVERT: F 368 ASP cc_start: 0.7949 (m-30) cc_final: 0.7540 (p0) REVERT: F 502 LYS cc_start: 0.8692 (mttt) cc_final: 0.8454 (tmtt) REVERT: I 543 ASN cc_start: 0.7918 (m-40) cc_final: 0.7510 (m-40) REVERT: I 581 LEU cc_start: 0.8421 (mt) cc_final: 0.8214 (pp) REVERT: I 601 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8099 (mtpp) REVERT: I 648 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8169 (pt0) outliers start: 39 outliers final: 25 residues processed: 217 average time/residue: 0.1337 time to fit residues: 42.1075 Evaluate side-chains 217 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 150 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 167 optimal weight: 20.0000 chunk 15 optimal weight: 0.2980 chunk 163 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN B 653 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN G 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102763 restraints weight = 25296.386| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.07 r_work: 0.3283 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15531 Z= 0.223 Angle : 0.695 17.810 21248 Z= 0.331 Chirality : 0.045 0.404 2603 Planarity : 0.004 0.063 2593 Dihedral : 6.351 54.831 3368 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.39 % Allowed : 10.10 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.21), residues: 1606 helix: 1.72 (0.27), residues: 395 sheet: 0.68 (0.25), residues: 417 loop : -0.80 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 617 TYR 0.015 0.002 TYR E 217 PHE 0.013 0.002 PHE E 317 TRP 0.022 0.002 TRP I 631 HIS 0.005 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00531 (15431) covalent geometry : angle 0.64866 (20981) SS BOND : bond 0.00457 ( 33) SS BOND : angle 1.74675 ( 66) hydrogen bonds : bond 0.04742 ( 468) hydrogen bonds : angle 4.85737 ( 1272) link_ALPHA1-3 : bond 0.01066 ( 4) link_ALPHA1-3 : angle 1.68687 ( 12) link_BETA1-4 : bond 0.00918 ( 17) link_BETA1-4 : angle 3.10343 ( 51) link_NAG-ASN : bond 0.00238 ( 46) link_NAG-ASN : angle 2.27551 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6749 (m-90) cc_final: 0.6139 (m-90) REVERT: A 94 ASN cc_start: 0.8934 (t0) cc_final: 0.8657 (t0) REVERT: A 268 GLU cc_start: 0.7443 (tp30) cc_final: 0.6863 (tt0) REVERT: A 475 MET cc_start: 0.8318 (mmm) cc_final: 0.7396 (mmm) REVERT: A 502 LYS cc_start: 0.8805 (mttt) cc_final: 0.8295 (ttmt) REVERT: A 503 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.5826 (tpp-160) REVERT: B 522 PHE cc_start: 0.8175 (t80) cc_final: 0.7368 (t80) REVERT: B 542 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6748 (ttp-110) REVERT: B 543 ASN cc_start: 0.8038 (m-40) cc_final: 0.7169 (m-40) REVERT: B 544 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8376 (mm) REVERT: B 591 GLN cc_start: 0.8268 (tt0) cc_final: 0.7568 (tp40) REVERT: B 654 GLU cc_start: 0.8222 (tp30) cc_final: 0.7951 (tp30) REVERT: E 51 THR cc_start: 0.9093 (m) cc_final: 0.8680 (p) REVERT: E 103 GLN cc_start: 0.7938 (tt0) cc_final: 0.7521 (tm-30) REVERT: E 232 LYS cc_start: 0.8238 (mttt) cc_final: 0.7279 (tptt) REVERT: E 325 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7231 (t-90) REVERT: G 590 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: G 648 GLU cc_start: 0.8454 (tp30) cc_final: 0.8166 (tp30) REVERT: F 66 HIS cc_start: 0.6123 (OUTLIER) cc_final: 0.5584 (t-90) REVERT: F 151 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7975 (ttm170) REVERT: F 211 GLU cc_start: 0.9105 (tt0) cc_final: 0.8678 (pt0) REVERT: F 368 ASP cc_start: 0.7971 (m-30) cc_final: 0.7530 (p0) REVERT: I 543 ASN cc_start: 0.7846 (m-40) cc_final: 0.7427 (m-40) REVERT: I 648 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8146 (pt0) outliers start: 35 outliers final: 22 residues processed: 214 average time/residue: 0.1291 time to fit residues: 40.4157 Evaluate side-chains 214 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 121 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN F 114 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.138203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105912 restraints weight = 25578.207| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.10 r_work: 0.3320 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15531 Z= 0.127 Angle : 0.611 17.586 21248 Z= 0.292 Chirality : 0.042 0.385 2603 Planarity : 0.003 0.047 2593 Dihedral : 5.765 56.579 3368 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.11 % Allowed : 11.19 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.21), residues: 1606 helix: 1.77 (0.27), residues: 412 sheet: 0.80 (0.25), residues: 417 loop : -0.66 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 617 TYR 0.016 0.001 TYR E 40 PHE 0.013 0.001 PHE A 53 TRP 0.023 0.001 TRP I 631 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00290 (15431) covalent geometry : angle 0.56776 (20981) SS BOND : bond 0.00329 ( 33) SS BOND : angle 1.39092 ( 66) hydrogen bonds : bond 0.04043 ( 468) hydrogen bonds : angle 4.56488 ( 1272) link_ALPHA1-3 : bond 0.01027 ( 4) link_ALPHA1-3 : angle 1.49490 ( 12) link_BETA1-4 : bond 0.01005 ( 17) link_BETA1-4 : angle 2.94185 ( 51) link_NAG-ASN : bond 0.00166 ( 46) link_NAG-ASN : angle 2.02510 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8938 (t0) cc_final: 0.8629 (t0) REVERT: A 106 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7315 (tt0) REVERT: A 268 GLU cc_start: 0.7387 (tp30) cc_final: 0.6723 (tt0) REVERT: A 475 MET cc_start: 0.8145 (mmm) cc_final: 0.7420 (mmm) REVERT: A 502 LYS cc_start: 0.8772 (mttt) cc_final: 0.8275 (ttmt) REVERT: A 503 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.5782 (tpp-160) REVERT: B 522 PHE cc_start: 0.8142 (t80) cc_final: 0.7457 (t80) REVERT: B 543 ASN cc_start: 0.8032 (m-40) cc_final: 0.7233 (m-40) REVERT: B 544 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8360 (mm) REVERT: E 51 THR cc_start: 0.9059 (m) cc_final: 0.8637 (p) REVERT: E 103 GLN cc_start: 0.7823 (tt0) cc_final: 0.7423 (tm-30) REVERT: E 199 SER cc_start: 0.9328 (p) cc_final: 0.9057 (m) REVERT: E 232 LYS cc_start: 0.8200 (mttt) cc_final: 0.7179 (tptt) REVERT: E 325 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7163 (t-90) REVERT: G 590 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6840 (mp10) REVERT: G 616 ASN cc_start: 0.7782 (p0) cc_final: 0.6801 (m110) REVERT: G 648 GLU cc_start: 0.8380 (tp30) cc_final: 0.8052 (tp30) REVERT: F 66 HIS cc_start: 0.6000 (OUTLIER) cc_final: 0.5500 (t-90) REVERT: F 151 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: F 162 THR cc_start: 0.9078 (m) cc_final: 0.8682 (p) REVERT: F 211 GLU cc_start: 0.9065 (tt0) cc_final: 0.8669 (pt0) REVERT: F 368 ASP cc_start: 0.7958 (m-30) cc_final: 0.7532 (p0) REVERT: F 502 LYS cc_start: 0.8475 (tttm) cc_final: 0.8238 (tmtt) REVERT: I 543 ASN cc_start: 0.7846 (m-40) cc_final: 0.7454 (m-40) REVERT: I 581 LEU cc_start: 0.8356 (mt) cc_final: 0.8112 (tp) REVERT: I 648 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8136 (pt0) outliers start: 31 outliers final: 20 residues processed: 224 average time/residue: 0.1084 time to fit residues: 35.7143 Evaluate side-chains 218 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 587 LEU Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 110 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN F 114 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.135912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103464 restraints weight = 25588.001| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.07 r_work: 0.3288 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15531 Z= 0.194 Angle : 0.663 17.547 21248 Z= 0.317 Chirality : 0.044 0.401 2603 Planarity : 0.004 0.057 2593 Dihedral : 5.850 51.061 3368 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.05 % Allowed : 11.87 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.21), residues: 1606 helix: 1.69 (0.27), residues: 412 sheet: 0.68 (0.25), residues: 417 loop : -0.71 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 617 TYR 0.015 0.001 TYR E 217 PHE 0.014 0.002 PHE A 53 TRP 0.039 0.002 TRP I 631 HIS 0.004 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00462 (15431) covalent geometry : angle 0.61915 (20981) SS BOND : bond 0.00388 ( 33) SS BOND : angle 1.55106 ( 66) hydrogen bonds : bond 0.04409 ( 468) hydrogen bonds : angle 4.70407 ( 1272) link_ALPHA1-3 : bond 0.00983 ( 4) link_ALPHA1-3 : angle 1.56065 ( 12) link_BETA1-4 : bond 0.00949 ( 17) link_BETA1-4 : angle 3.02102 ( 51) link_NAG-ASN : bond 0.00216 ( 46) link_NAG-ASN : angle 2.15278 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8956 (t0) cc_final: 0.8650 (t0) REVERT: A 207 LYS cc_start: 0.7214 (tmtt) cc_final: 0.6930 (tmtt) REVERT: A 268 GLU cc_start: 0.7371 (tp30) cc_final: 0.6914 (tt0) REVERT: A 475 MET cc_start: 0.8235 (mmm) cc_final: 0.7377 (mmm) REVERT: A 502 LYS cc_start: 0.8803 (mttt) cc_final: 0.8259 (ttmt) REVERT: A 503 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.5772 (tpp-160) REVERT: B 522 PHE cc_start: 0.8148 (t80) cc_final: 0.7560 (t80) REVERT: B 542 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6734 (ttp-110) REVERT: B 543 ASN cc_start: 0.7980 (m-40) cc_final: 0.7257 (m-40) REVERT: E 51 THR cc_start: 0.9066 (m) cc_final: 0.8669 (p) REVERT: E 103 GLN cc_start: 0.7856 (tt0) cc_final: 0.7454 (tm-30) REVERT: E 232 LYS cc_start: 0.8263 (mttt) cc_final: 0.7244 (tptt) REVERT: E 325 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7219 (t-90) REVERT: E 434 MET cc_start: 0.8964 (ttp) cc_final: 0.8731 (ttt) REVERT: G 590 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: G 616 ASN cc_start: 0.7856 (p0) cc_final: 0.6815 (m110) REVERT: G 648 GLU cc_start: 0.8371 (tp30) cc_final: 0.8032 (tp30) REVERT: F 66 HIS cc_start: 0.6032 (OUTLIER) cc_final: 0.5522 (t-90) REVERT: F 151 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7847 (ttm170) REVERT: F 211 GLU cc_start: 0.9111 (tt0) cc_final: 0.8686 (pt0) REVERT: F 368 ASP cc_start: 0.7949 (m-30) cc_final: 0.7502 (p0) REVERT: I 543 ASN cc_start: 0.7802 (m-40) cc_final: 0.7400 (m-40) REVERT: I 648 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8145 (pt0) outliers start: 30 outliers final: 23 residues processed: 208 average time/residue: 0.1415 time to fit residues: 42.4691 Evaluate side-chains 215 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 587 LEU Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 653 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN G 651 ASN F 114 GLN ** F 289 ASN ** 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 = 0.3857 r_free = 0.3857 target = 0.136427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103986 restraints weight = 25575.553| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.08 r_work: 0.3299 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15531 Z= 0.170 Angle : 0.647 17.668 21248 Z= 0.308 Chirality : 0.043 0.397 2603 Planarity : 0.003 0.039 2593 Dihedral : 5.712 50.656 3368 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.05 % Allowed : 11.66 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.21), residues: 1606 helix: 1.69 (0.27), residues: 412 sheet: 0.65 (0.25), residues: 417 loop : -0.73 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 617 TYR 0.013 0.001 TYR E 217 PHE 0.019 0.002 PHE A 53 TRP 0.035 0.002 TRP I 631 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00400 (15431) covalent geometry : angle 0.60463 (20981) SS BOND : bond 0.00343 ( 33) SS BOND : angle 1.40615 ( 66) hydrogen bonds : bond 0.04284 ( 468) hydrogen bonds : angle 4.64304 ( 1272) link_ALPHA1-3 : bond 0.00990 ( 4) link_ALPHA1-3 : angle 1.53764 ( 12) link_BETA1-4 : bond 0.00956 ( 17) link_BETA1-4 : angle 2.99656 ( 51) link_NAG-ASN : bond 0.00169 ( 46) link_NAG-ASN : angle 2.10683 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8929 (t0) cc_final: 0.8641 (t0) REVERT: A 207 LYS cc_start: 0.7251 (tmtt) cc_final: 0.6975 (tmtt) REVERT: A 268 GLU cc_start: 0.7349 (tp30) cc_final: 0.6864 (tt0) REVERT: A 475 MET cc_start: 0.8201 (mmm) cc_final: 0.7346 (mmm) REVERT: A 502 LYS cc_start: 0.8781 (mttt) cc_final: 0.8239 (ttmt) REVERT: A 503 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.5784 (tpp-160) REVERT: B 522 PHE cc_start: 0.8145 (t80) cc_final: 0.7560 (t80) REVERT: B 542 ARG cc_start: 0.6953 (mtm-85) cc_final: 0.6745 (ttp-110) REVERT: B 543 ASN cc_start: 0.8055 (m-40) cc_final: 0.7357 (m-40) REVERT: B 591 GLN cc_start: 0.8227 (tt0) cc_final: 0.7428 (tp40) REVERT: E 51 THR cc_start: 0.9072 (m) cc_final: 0.8694 (p) REVERT: E 103 GLN cc_start: 0.7796 (tt0) cc_final: 0.7393 (tm-30) REVERT: E 232 LYS cc_start: 0.8258 (mttt) cc_final: 0.7190 (tptt) REVERT: E 325 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7231 (t-90) REVERT: E 434 MET cc_start: 0.8959 (ttp) cc_final: 0.8729 (ttt) REVERT: G 590 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: G 648 GLU cc_start: 0.8376 (tp30) cc_final: 0.8030 (tp30) REVERT: F 66 HIS cc_start: 0.6049 (OUTLIER) cc_final: 0.5545 (t-90) REVERT: F 151 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7976 (ttm170) REVERT: F 211 GLU cc_start: 0.9109 (tt0) cc_final: 0.8677 (pt0) REVERT: F 368 ASP cc_start: 0.7954 (m-30) cc_final: 0.7507 (p0) REVERT: I 543 ASN cc_start: 0.7807 (m-40) cc_final: 0.7407 (m-40) REVERT: I 648 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8141 (pt0) outliers start: 30 outliers final: 23 residues processed: 207 average time/residue: 0.1412 time to fit residues: 42.3806 Evaluate side-chains 213 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 587 LEU Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 641 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN F 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106338 restraints weight = 25379.094| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.12 r_work: 0.3325 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15531 Z= 0.119 Angle : 0.618 17.535 21248 Z= 0.294 Chirality : 0.042 0.388 2603 Planarity : 0.004 0.054 2593 Dihedral : 5.456 48.364 3368 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.77 % Allowed : 11.94 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.21), residues: 1606 helix: 1.73 (0.27), residues: 412 sheet: 0.72 (0.25), residues: 417 loop : -0.68 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 617 TYR 0.012 0.001 TYR E 40 PHE 0.018 0.001 PHE A 53 TRP 0.034 0.001 TRP I 631 HIS 0.003 0.001 HIS I 585 Details of bonding type rmsd covalent geometry : bond 0.00269 (15431) covalent geometry : angle 0.57796 (20981) SS BOND : bond 0.00271 ( 33) SS BOND : angle 1.23514 ( 66) hydrogen bonds : bond 0.03979 ( 468) hydrogen bonds : angle 4.52955 ( 1272) link_ALPHA1-3 : bond 0.00943 ( 4) link_ALPHA1-3 : angle 1.46090 ( 12) link_BETA1-4 : bond 0.01002 ( 17) link_BETA1-4 : angle 2.91488 ( 51) link_NAG-ASN : bond 0.00141 ( 46) link_NAG-ASN : angle 2.00239 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3422.29 seconds wall clock time: 59 minutes 28.19 seconds (3568.19 seconds total)