Starting phenix.real_space_refine on Fri Jun 13 18:57:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f9g_28942/06_2025/8f9g_28942.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f9g_28942/06_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_28942/06_2025/8f9g_28942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f9g_28942/06_2025/8f9g_28942.map" model { file = "/net/cci-nas-00/data/ceres_data/8f9g_28942/06_2025/8f9g_28942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f9g_28942/06_2025/8f9g_28942.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.46, per 1000 atoms: 0.76 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: 4.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.62 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: 4.83 Time building geometry restraints manager: 5.21 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 504 or resid 601 through 609)) selection = (chain 'F' and (resid 33 through 504 or resid 601 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 662 or resid 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: 7.750 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 38.710 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.028 0.003 TRP F 479 HIS 0.007 0.001 HIS F 374 PHE 0.032 0.003 PHE E 383 TYR 0.021 0.003 TYR F 191 ARG 0.012 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 46) link_NAG-ASN : angle 3.56351 ( 138) link_BETA1-4 : bond 0.00859 ( 17) link_BETA1-4 : angle 3.37027 ( 51) link_ALPHA1-3 : bond 0.00489 ( 4) link_ALPHA1-3 : angle 2.18651 ( 12) hydrogen bonds : bond 0.15388 ( 468) hydrogen bonds : angle 7.41081 ( 1272) SS BOND : bond 0.00467 ( 33) SS BOND : angle 2.47109 ( 66) covalent geometry : bond 0.00639 (15431) covalent geometry : angle 1.03608 (20981) *********************** 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 : 1.902 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: 0.7970 (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: 0.7055 (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: 0.7544 (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: 0.6935 (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 649 SER cc_start: 0.7785 (t) cc_final: 0.7531 (t) 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 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: 0.7025 (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: 0.2846 time to fit residues: 159.0347 Evaluate side-chains 225 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 155 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 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 = 0.3940 r_free = 0.3940 target = 0.143155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110667 restraints weight = 25025.246| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.15 r_work: 0.3390 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2191 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= 0.171 Angle : 0.716 17.221 21248 Z= 0.344 Chirality : 0.045 0.443 2603 Planarity : 0.004 0.043 2593 Dihedral : 8.956 68.295 3369 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 7.44 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1606 helix: 1.50 (0.25), residues: 452 sheet: 1.08 (0.24), residues: 405 loop : 0.32 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 479 HIS 0.004 0.001 HIS A 105 PHE 0.023 0.002 PHE F 53 TYR 0.013 0.001 TYR A 217 ARG 0.005 0.001 ARG F 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 46) link_NAG-ASN : angle 2.73755 ( 138) link_BETA1-4 : bond 0.01024 ( 17) link_BETA1-4 : angle 3.03568 ( 51) link_ALPHA1-3 : bond 0.00879 ( 4) link_ALPHA1-3 : angle 2.55323 ( 12) hydrogen bonds : bond 0.05872 ( 468) hydrogen bonds : angle 5.25344 ( 1272) SS BOND : bond 0.00525 ( 33) SS BOND : angle 1.48177 ( 66) covalent geometry : bond 0.00392 (15431) covalent geometry : angle 0.66115 (20981) *********************** 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 : 1.759 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7380 (mm-30) REVERT: A 107 ASP cc_start: 0.8487 (m-30) cc_final: 0.8275 (m-30) REVERT: A 340 GLU cc_start: 0.8445 (tt0) cc_final: 0.8005 (tp30) REVERT: A 349 LEU cc_start: 0.8549 (mt) cc_final: 0.8343 (mt) REVERT: A 475 MET cc_start: 0.8188 (mmm) cc_final: 0.7412 (mmm) REVERT: B 522 PHE cc_start: 0.8124 (t80) cc_final: 0.7661 (t80) REVERT: B 543 ASN cc_start: 0.7992 (m-40) cc_final: 0.7316 (m-40) REVERT: E 103 GLN cc_start: 0.7922 (tt0) cc_final: 0.7560 (tm-30) REVERT: E 154 ILE cc_start: 0.8948 (mt) cc_final: 0.8660 (mt) REVERT: E 199 SER cc_start: 0.9286 (p) cc_final: 0.8785 (m) REVERT: E 232 LYS cc_start: 0.7777 (mttt) cc_final: 0.7133 (tptt) REVERT: E 280 ASN cc_start: 0.8556 (m-40) cc_final: 0.8290 (m-40) REVERT: E 502 LYS cc_start: 0.8465 (pttm) cc_final: 0.8163 (tmtt) REVERT: G 590 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6705 (mp10) REVERT: G 636 SER cc_start: 0.9108 (t) cc_final: 0.8677 (m) REVERT: F 66 HIS cc_start: 0.6035 (OUTLIER) cc_final: 0.5466 (t-90) REVERT: F 211 GLU cc_start: 0.9049 (tt0) cc_final: 0.8620 (pt0) REVERT: F 327 ARG cc_start: 0.7982 (mtt90) cc_final: 0.7473 (mtp85) REVERT: F 368 ASP cc_start: 0.8039 (m-30) cc_final: 0.7573 (p0) REVERT: I 539 VAL cc_start: 0.8447 (t) cc_final: 0.7962 (t) REVERT: I 543 ASN cc_start: 0.7867 (m-40) cc_final: 0.7358 (m110) REVERT: I 607 ASN cc_start: 0.8453 (m-40) cc_final: 0.7976 (m-40) REVERT: I 624 ASP cc_start: 0.8290 (m-30) cc_final: 0.7865 (m-30) REVERT: I 636 SER cc_start: 0.8300 (t) cc_final: 0.8087 (m) REVERT: I 648 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8241 (pt0) outliers start: 28 outliers final: 13 residues processed: 256 average time/residue: 0.2814 time to fit residues: 105.6961 Evaluate side-chains 219 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 115 SER 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 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 115 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 85 HIS E 195 ASN E 249 HIS G 616 ASN G 653 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107907 restraints weight = 25132.839| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.14 r_work: 0.3352 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2852 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= 0.166 Angle : 0.657 17.681 21248 Z= 0.315 Chirality : 0.044 0.414 2603 Planarity : 0.004 0.040 2593 Dihedral : 7.090 55.462 3368 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.73 % Allowed : 8.05 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1606 helix: 1.38 (0.26), residues: 454 sheet: 1.06 (0.24), residues: 453 loop : -0.05 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 479 HIS 0.005 0.001 HIS F 85 PHE 0.025 0.002 PHE F 53 TYR 0.011 0.001 TYR E 39 ARG 0.006 0.001 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 46) link_NAG-ASN : angle 2.36488 ( 138) link_BETA1-4 : bond 0.00959 ( 17) link_BETA1-4 : angle 2.98079 ( 51) link_ALPHA1-3 : bond 0.01173 ( 4) link_ALPHA1-3 : angle 1.85659 ( 12) hydrogen bonds : bond 0.04815 ( 468) hydrogen bonds : angle 4.81112 ( 1272) SS BOND : bond 0.00592 ( 33) SS BOND : angle 1.44498 ( 66) covalent geometry : bond 0.00385 (15431) covalent geometry : angle 0.60836 (20981) *********************** 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 266 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 2.743 Fit side-chains revert: symmetry clash REVERT: A 502 LYS cc_start: 0.8719 (mttt) cc_final: 0.8156 (ttmt) REVERT: A 503 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6029 (tpp-160) REVERT: B 522 PHE cc_start: 0.8174 (t80) cc_final: 0.7663 (t80) REVERT: B 543 ASN cc_start: 0.8007 (m-40) cc_final: 0.7313 (m-40) REVERT: B 544 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8092 (mm) REVERT: E 51 THR cc_start: 0.8952 (m) cc_final: 0.8497 (p) REVERT: E 103 GLN cc_start: 0.7921 (tt0) cc_final: 0.7547 (tm-30) REVERT: E 199 SER cc_start: 0.9353 (p) cc_final: 0.9044 (p) REVERT: E 232 LYS cc_start: 0.7969 (mttt) cc_final: 0.7207 (tptt) REVERT: E 280 ASN cc_start: 0.8563 (m-40) cc_final: 0.8283 (m-40) REVERT: G 590 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.6719 (mp10) REVERT: G 653 GLN cc_start: 0.7074 (mt0) cc_final: 0.6786 (mt0) REVERT: F 66 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5525 (t-90) REVERT: F 161 MET cc_start: 0.8579 (tpt) cc_final: 0.8170 (tpt) REVERT: F 211 GLU cc_start: 0.9052 (tt0) cc_final: 0.8636 (pt0) REVERT: F 368 ASP cc_start: 0.7964 (m-30) cc_final: 0.7528 (p0) REVERT: I 539 VAL cc_start: 0.8377 (t) cc_final: 0.7879 (t) REVERT: I 543 ASN cc_start: 0.7927 (m-40) cc_final: 0.7450 (m110) REVERT: I 607 ASN cc_start: 0.8536 (m-40) cc_final: 0.8060 (m-40) REVERT: I 624 ASP cc_start: 0.8188 (m-30) cc_final: 0.7874 (m-30) REVERT: I 648 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8173 (pt0) outliers start: 40 outliers final: 21 residues processed: 246 average time/residue: 0.3072 time to fit residues: 110.5083 Evaluate side-chains 229 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 2.997 ------------------------------------------------------------------------------- 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 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 346 VAL 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 53 optimal weight: 4.9990 chunk 63 optimal weight: 0.0970 chunk 168 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 167 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 195 ASN ** E 302 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 = 0.3886 r_free = 0.3886 target = 0.138619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105660 restraints weight = 25159.710| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.12 r_work: 0.3328 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15531 Z= 0.181 Angle : 0.660 17.592 21248 Z= 0.317 Chirality : 0.044 0.412 2603 Planarity : 0.003 0.039 2593 Dihedral : 6.472 59.588 3368 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.66 % Allowed : 8.46 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1606 helix: 1.54 (0.27), residues: 436 sheet: 1.25 (0.24), residues: 423 loop : -0.32 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 69 HIS 0.005 0.001 HIS F 85 PHE 0.027 0.002 PHE F 53 TYR 0.011 0.001 TYR E 217 ARG 0.004 0.000 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 46) link_NAG-ASN : angle 2.20460 ( 138) link_BETA1-4 : bond 0.00999 ( 17) link_BETA1-4 : angle 2.98695 ( 51) link_ALPHA1-3 : bond 0.01168 ( 4) link_ALPHA1-3 : angle 1.82163 ( 12) hydrogen bonds : bond 0.04540 ( 468) hydrogen bonds : angle 4.69588 ( 1272) SS BOND : bond 0.00371 ( 33) SS BOND : angle 1.34412 ( 66) covalent geometry : bond 0.00425 (15431) covalent geometry : angle 0.61656 (20981) *********************** 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 242 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7420 (tt0) REVERT: A 425 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7875 (t0) REVERT: A 475 MET cc_start: 0.8218 (mmm) cc_final: 0.7273 (mmm) REVERT: A 502 LYS cc_start: 0.8716 (mttt) cc_final: 0.8170 (ttmt) REVERT: A 503 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.5916 (tpp-160) REVERT: B 522 PHE cc_start: 0.8219 (t80) cc_final: 0.7473 (t80) REVERT: B 543 ASN cc_start: 0.8049 (m-40) cc_final: 0.7205 (m-40) REVERT: B 591 GLN cc_start: 0.8114 (tt0) cc_final: 0.7560 (tp40) REVERT: E 51 THR cc_start: 0.8995 (m) cc_final: 0.8536 (p) REVERT: E 103 GLN cc_start: 0.7938 (tt0) cc_final: 0.7555 (tm-30) REVERT: E 232 LYS cc_start: 0.8079 (mttt) cc_final: 0.7251 (tptt) REVERT: E 280 ASN cc_start: 0.8604 (m-40) cc_final: 0.8300 (m-40) REVERT: E 325 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7253 (t-90) REVERT: G 590 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: G 653 GLN cc_start: 0.7050 (mt0) cc_final: 0.6804 (mt0) REVERT: F 66 HIS cc_start: 0.6060 (OUTLIER) cc_final: 0.5496 (t-90) REVERT: F 125 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8226 (mt) REVERT: F 151 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7635 (ttm170) REVERT: F 161 MET cc_start: 0.8616 (tpt) cc_final: 0.8315 (tpt) REVERT: F 211 GLU cc_start: 0.9067 (tt0) cc_final: 0.8646 (pt0) REVERT: F 368 ASP cc_start: 0.8042 (m-30) cc_final: 0.7602 (p0) REVERT: I 543 ASN cc_start: 0.7957 (m-40) cc_final: 0.7476 (m110) REVERT: I 607 ASN cc_start: 0.8562 (m-40) cc_final: 0.8293 (m-40) REVERT: I 624 ASP cc_start: 0.8181 (m-30) cc_final: 0.7866 (m-30) REVERT: I 648 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8125 (pt0) outliers start: 39 outliers final: 23 residues processed: 224 average time/residue: 0.3219 time to fit residues: 107.0739 Evaluate side-chains 225 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 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 648 GLU 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 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 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 125 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105462 restraints weight = 25467.825| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.14 r_work: 0.3325 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15531 Z= 0.167 Angle : 0.630 17.502 21248 Z= 0.303 Chirality : 0.043 0.401 2603 Planarity : 0.003 0.054 2593 Dihedral : 6.248 58.585 3368 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.05 % Allowed : 9.07 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1606 helix: 1.86 (0.27), residues: 412 sheet: 1.18 (0.25), residues: 423 loop : -0.35 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 631 HIS 0.004 0.001 HIS F 374 PHE 0.018 0.002 PHE F 53 TYR 0.011 0.001 TYR E 217 ARG 0.006 0.000 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 46) link_NAG-ASN : angle 2.13186 ( 138) link_BETA1-4 : bond 0.00963 ( 17) link_BETA1-4 : angle 2.95731 ( 51) link_ALPHA1-3 : bond 0.01158 ( 4) link_ALPHA1-3 : angle 1.72496 ( 12) hydrogen bonds : bond 0.04402 ( 468) hydrogen bonds : angle 4.61824 ( 1272) SS BOND : bond 0.00375 ( 33) SS BOND : angle 1.66409 ( 66) covalent geometry : bond 0.00391 (15431) covalent geometry : angle 0.58357 (20981) *********************** 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 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7392 (tt0) REVERT: A 475 MET cc_start: 0.8186 (mmm) cc_final: 0.7220 (mmm) REVERT: A 502 LYS cc_start: 0.8735 (mttt) cc_final: 0.8173 (ttmt) REVERT: A 503 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.5777 (tpp-160) REVERT: B 522 PHE cc_start: 0.8180 (t80) cc_final: 0.7387 (t80) REVERT: B 543 ASN cc_start: 0.8092 (m-40) cc_final: 0.7163 (m-40) REVERT: B 544 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8210 (mm) REVERT: B 591 GLN cc_start: 0.8116 (tt0) cc_final: 0.7406 (tp40) REVERT: E 51 THR cc_start: 0.9024 (m) cc_final: 0.8558 (p) REVERT: E 103 GLN cc_start: 0.7901 (tt0) cc_final: 0.7515 (tm-30) REVERT: E 232 LYS cc_start: 0.8057 (mttt) cc_final: 0.7272 (tptt) REVERT: E 280 ASN cc_start: 0.8624 (m-40) cc_final: 0.8310 (m-40) REVERT: E 325 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7192 (t-90) REVERT: G 590 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: F 66 HIS cc_start: 0.6055 (OUTLIER) cc_final: 0.5505 (t-90) REVERT: F 151 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7570 (ttm170) REVERT: F 161 MET cc_start: 0.8649 (tpt) cc_final: 0.8383 (tpt) REVERT: F 211 GLU cc_start: 0.9071 (tt0) cc_final: 0.8655 (pt0) REVERT: F 368 ASP cc_start: 0.8063 (m-30) cc_final: 0.7610 (p0) REVERT: F 502 LYS cc_start: 0.8562 (mttt) cc_final: 0.8315 (tmtt) REVERT: I 543 ASN cc_start: 0.7887 (m-40) cc_final: 0.7419 (m110) REVERT: I 601 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8124 (mtpp) REVERT: I 624 ASP cc_start: 0.8159 (m-30) cc_final: 0.7787 (m-30) REVERT: I 648 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8148 (pt0) outliers start: 30 outliers final: 21 residues processed: 226 average time/residue: 0.3160 time to fit residues: 105.1015 Evaluate side-chains 219 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 602 LEU Chi-restraints excluded: chain B residue 660 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 141 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN 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 = 0.3840 r_free = 0.3840 target = 0.135026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102530 restraints weight = 25483.462| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.05 r_work: 0.3281 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 15531 Z= 0.262 Angle : 0.727 17.503 21248 Z= 0.348 Chirality : 0.046 0.417 2603 Planarity : 0.004 0.050 2593 Dihedral : 6.576 58.351 3368 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.59 % Allowed : 9.14 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1606 helix: 1.58 (0.27), residues: 412 sheet: 0.83 (0.25), residues: 423 loop : -0.63 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 631 HIS 0.007 0.001 HIS F 85 PHE 0.023 0.002 PHE F 53 TYR 0.018 0.002 TYR E 217 ARG 0.007 0.001 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 46) link_NAG-ASN : angle 2.35478 ( 138) link_BETA1-4 : bond 0.00851 ( 17) link_BETA1-4 : angle 3.11539 ( 51) link_ALPHA1-3 : bond 0.01069 ( 4) link_ALPHA1-3 : angle 1.69991 ( 12) hydrogen bonds : bond 0.04963 ( 468) hydrogen bonds : angle 4.90043 ( 1272) SS BOND : bond 0.00547 ( 33) SS BOND : angle 1.70860 ( 66) covalent geometry : bond 0.00630 (15431) covalent geometry : angle 0.68127 (20981) *********************** 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 233 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6780 (m-90) cc_final: 0.6170 (m-90) REVERT: A 94 ASN cc_start: 0.8965 (t0) cc_final: 0.8670 (t0) REVERT: A 246 GLN cc_start: 0.6295 (pm20) cc_final: 0.6092 (mp10) REVERT: A 425 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7936 (t0) REVERT: A 502 LYS cc_start: 0.8803 (mttt) cc_final: 0.8327 (ttmt) REVERT: A 503 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.5879 (tpp-160) REVERT: B 522 PHE cc_start: 0.8203 (t80) cc_final: 0.7515 (t80) REVERT: B 544 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 591 GLN cc_start: 0.8292 (tt0) cc_final: 0.7707 (tp40) REVERT: E 51 THR cc_start: 0.9106 (m) cc_final: 0.8703 (p) REVERT: E 103 GLN cc_start: 0.8006 (tt0) cc_final: 0.7603 (tm-30) REVERT: E 232 LYS cc_start: 0.8237 (mttt) cc_final: 0.7344 (tptt) REVERT: E 325 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7163 (t-90) REVERT: G 590 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: F 66 HIS cc_start: 0.6206 (OUTLIER) cc_final: 0.5662 (t-90) REVERT: F 151 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: F 161 MET cc_start: 0.8685 (tpt) cc_final: 0.8431 (tpt) REVERT: F 211 GLU cc_start: 0.9084 (tt0) cc_final: 0.8694 (pt0) REVERT: F 368 ASP cc_start: 0.7954 (m-30) cc_final: 0.7551 (p0) REVERT: I 543 ASN cc_start: 0.7871 (m-40) cc_final: 0.7451 (m-40) REVERT: I 581 LEU cc_start: 0.8417 (mt) cc_final: 0.8205 (pp) REVERT: I 624 ASP cc_start: 0.8168 (m-30) cc_final: 0.7812 (m-30) REVERT: I 648 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8162 (pt0) outliers start: 38 outliers final: 23 residues processed: 219 average time/residue: 0.2851 time to fit residues: 90.4735 Evaluate side-chains 219 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 111 optimal weight: 0.0470 chunk 182 optimal weight: 30.0000 chunk 78 optimal weight: 0.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- 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 195 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3868 r_free = 0.3868 target = 0.137131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104505 restraints weight = 25486.207| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.10 r_work: 0.3305 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15531 Z= 0.153 Angle : 0.625 17.650 21248 Z= 0.300 Chirality : 0.043 0.390 2603 Planarity : 0.003 0.052 2593 Dihedral : 6.076 57.458 3368 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.84 % Allowed : 10.50 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1606 helix: 1.73 (0.27), residues: 412 sheet: 0.87 (0.25), residues: 417 loop : -0.64 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 631 HIS 0.003 0.001 HIS F 216 PHE 0.020 0.002 PHE F 53 TYR 0.012 0.001 TYR E 217 ARG 0.006 0.000 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 46) link_NAG-ASN : angle 2.12990 ( 138) link_BETA1-4 : bond 0.00984 ( 17) link_BETA1-4 : angle 2.98806 ( 51) link_ALPHA1-3 : bond 0.01069 ( 4) link_ALPHA1-3 : angle 1.59718 ( 12) hydrogen bonds : bond 0.04290 ( 468) hydrogen bonds : angle 4.63813 ( 1272) SS BOND : bond 0.00361 ( 33) SS BOND : angle 1.52148 ( 66) covalent geometry : bond 0.00359 (15431) covalent geometry : angle 0.57852 (20981) *********************** 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 225 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.5514 (m) cc_final: 0.5121 (t) REVERT: A 94 ASN cc_start: 0.8916 (t0) cc_final: 0.8645 (t0) REVERT: A 475 MET cc_start: 0.8189 (mmm) cc_final: 0.7440 (mmm) REVERT: A 502 LYS cc_start: 0.8780 (mttt) cc_final: 0.8262 (ttmt) REVERT: A 503 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.5827 (tpp-160) REVERT: B 522 PHE cc_start: 0.8140 (t80) cc_final: 0.7442 (t80) REVERT: B 543 ASN cc_start: 0.8023 (m-40) cc_final: 0.7191 (m-40) REVERT: B 544 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8339 (mm) REVERT: B 591 GLN cc_start: 0.8156 (tt0) cc_final: 0.7437 (tp40) REVERT: B 654 GLU cc_start: 0.8206 (tp30) cc_final: 0.7959 (tp30) REVERT: E 51 THR cc_start: 0.9053 (m) cc_final: 0.8621 (p) REVERT: E 82 GLN cc_start: 0.7894 (pp30) cc_final: 0.7389 (pp30) REVERT: E 103 GLN cc_start: 0.7857 (tt0) cc_final: 0.7442 (tm-30) REVERT: E 232 LYS cc_start: 0.8218 (mttt) cc_final: 0.7216 (tptt) REVERT: E 325 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.7185 (t-90) REVERT: G 590 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6829 (mp10) REVERT: F 66 HIS cc_start: 0.6030 (OUTLIER) cc_final: 0.5519 (t-90) REVERT: F 151 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7941 (ttm170) REVERT: F 161 MET cc_start: 0.8597 (tpt) cc_final: 0.8366 (tpt) REVERT: F 211 GLU cc_start: 0.9089 (tt0) cc_final: 0.8682 (pt0) REVERT: F 368 ASP cc_start: 0.7958 (m-30) cc_final: 0.7524 (p0) REVERT: F 426 MET cc_start: 0.7987 (mtp) cc_final: 0.7711 (mtp) REVERT: F 475 MET cc_start: 0.8644 (mmt) cc_final: 0.8172 (mmm) REVERT: I 543 ASN cc_start: 0.7845 (m-40) cc_final: 0.7416 (m-40) REVERT: I 624 ASP cc_start: 0.8124 (m-30) cc_final: 0.7774 (m-30) REVERT: I 648 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8136 (pt0) outliers start: 27 outliers final: 18 residues processed: 215 average time/residue: 0.3096 time to fit residues: 95.1200 Evaluate side-chains 213 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 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 325 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 67 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN E 195 ASN ** E 374 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.137038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104538 restraints weight = 25332.109| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.09 r_work: 0.3301 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15531 Z= 0.161 Angle : 0.628 17.519 21248 Z= 0.300 Chirality : 0.043 0.394 2603 Planarity : 0.003 0.047 2593 Dihedral : 5.844 55.415 3368 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.98 % Allowed : 10.71 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1606 helix: 1.73 (0.27), residues: 413 sheet: 0.96 (0.26), residues: 402 loop : -0.67 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 69 HIS 0.004 0.001 HIS F 216 PHE 0.017 0.002 PHE A 53 TYR 0.013 0.001 TYR E 217 ARG 0.006 0.000 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 46) link_NAG-ASN : angle 2.10645 ( 138) link_BETA1-4 : bond 0.00950 ( 17) link_BETA1-4 : angle 2.97846 ( 51) link_ALPHA1-3 : bond 0.01029 ( 4) link_ALPHA1-3 : angle 1.54120 ( 12) hydrogen bonds : bond 0.04218 ( 468) hydrogen bonds : angle 4.58836 ( 1272) SS BOND : bond 0.00356 ( 33) SS BOND : angle 1.50388 ( 66) covalent geometry : bond 0.00379 (15431) covalent geometry : angle 0.58274 (20981) *********************** 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 230 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 1.819 Fit side-chains revert: symmetry clash REVERT: A 54 CYS cc_start: 0.5580 (m) cc_final: 0.5083 (t) REVERT: A 94 ASN cc_start: 0.8958 (t0) cc_final: 0.8687 (t0) REVERT: A 207 LYS cc_start: 0.7315 (tmtt) cc_final: 0.6883 (tmtt) REVERT: A 475 MET cc_start: 0.8139 (mmm) cc_final: 0.7287 (mmm) REVERT: A 502 LYS cc_start: 0.8801 (mttt) cc_final: 0.8253 (ttmt) REVERT: A 503 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.5764 (tpp-160) REVERT: B 522 PHE cc_start: 0.8157 (t80) cc_final: 0.7454 (t80) REVERT: B 543 ASN cc_start: 0.8017 (m-40) cc_final: 0.7195 (m-40) REVERT: B 591 GLN cc_start: 0.8095 (tt0) cc_final: 0.7417 (tp40) REVERT: E 51 THR cc_start: 0.9062 (m) cc_final: 0.8652 (p) REVERT: E 82 GLN cc_start: 0.7842 (pp30) cc_final: 0.7338 (pp30) REVERT: E 103 GLN cc_start: 0.7893 (tt0) cc_final: 0.7491 (tm-30) REVERT: E 232 LYS cc_start: 0.8258 (mttt) cc_final: 0.7204 (tptt) REVERT: E 325 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7195 (t-90) REVERT: G 530 MET cc_start: 0.8068 (tpp) cc_final: 0.7768 (mtt) REVERT: G 590 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6860 (mp10) REVERT: F 66 HIS cc_start: 0.6051 (OUTLIER) cc_final: 0.5543 (t-90) REVERT: F 151 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7936 (ttm170) REVERT: F 161 MET cc_start: 0.8620 (tpt) cc_final: 0.8369 (tpt) REVERT: F 211 GLU cc_start: 0.9081 (tt0) cc_final: 0.8674 (pt0) REVERT: F 368 ASP cc_start: 0.7961 (m-30) cc_final: 0.7523 (p0) REVERT: F 475 MET cc_start: 0.8649 (mmt) cc_final: 0.8323 (mmm) REVERT: I 543 ASN cc_start: 0.7805 (m-40) cc_final: 0.7384 (m-40) REVERT: I 624 ASP cc_start: 0.8123 (m-30) cc_final: 0.7779 (m-30) REVERT: I 648 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8138 (pt0) outliers start: 29 outliers final: 21 residues processed: 218 average time/residue: 0.3181 time to fit residues: 100.2634 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 : 1.567 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 503 ARG 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 146 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103600 restraints weight = 25351.966| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.02 r_work: 0.3302 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15531 Z= 0.189 Angle : 0.654 17.605 21248 Z= 0.314 Chirality : 0.044 0.400 2603 Planarity : 0.003 0.048 2593 Dihedral : 5.833 51.003 3368 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.18 % Allowed : 10.64 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1606 helix: 1.64 (0.27), residues: 413 sheet: 0.64 (0.25), residues: 435 loop : -0.67 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 631 HIS 0.004 0.001 HIS F 216 PHE 0.017 0.002 PHE F 53 TYR 0.014 0.001 TYR E 217 ARG 0.009 0.001 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 46) link_NAG-ASN : angle 2.16060 ( 138) link_BETA1-4 : bond 0.00964 ( 17) link_BETA1-4 : angle 3.01469 ( 51) link_ALPHA1-3 : bond 0.01046 ( 4) link_ALPHA1-3 : angle 1.56930 ( 12) hydrogen bonds : bond 0.04336 ( 468) hydrogen bonds : angle 4.65459 ( 1272) SS BOND : bond 0.00408 ( 33) SS BOND : angle 1.50204 ( 66) covalent geometry : bond 0.00449 (15431) covalent geometry : angle 0.60983 (20981) *********************** 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 225 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 54 CYS cc_start: 0.5595 (m) cc_final: 0.5166 (t) REVERT: A 94 ASN cc_start: 0.8952 (t0) cc_final: 0.8706 (t0) REVERT: A 207 LYS cc_start: 0.7436 (tmtt) cc_final: 0.7077 (tmtt) REVERT: A 425 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7854 (t0) REVERT: A 475 MET cc_start: 0.8209 (mmm) cc_final: 0.7343 (mmm) REVERT: A 502 LYS cc_start: 0.8771 (mttt) cc_final: 0.8259 (ttmt) REVERT: A 503 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.5826 (tpp-160) REVERT: B 522 PHE cc_start: 0.8182 (t80) cc_final: 0.7556 (t80) REVERT: B 543 ASN cc_start: 0.8081 (m-40) cc_final: 0.7349 (m-40) REVERT: B 591 GLN cc_start: 0.8165 (tt0) cc_final: 0.7486 (tp40) REVERT: E 51 THR cc_start: 0.9090 (m) cc_final: 0.8702 (p) REVERT: E 82 GLN cc_start: 0.7835 (pp30) cc_final: 0.7359 (pp30) REVERT: E 103 GLN cc_start: 0.7898 (tt0) cc_final: 0.7516 (tm-30) REVERT: E 232 LYS cc_start: 0.8256 (mttt) cc_final: 0.7261 (tptt) REVERT: E 325 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7201 (t-90) REVERT: G 530 MET cc_start: 0.8101 (tpp) cc_final: 0.7855 (mtt) REVERT: G 590 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: F 66 HIS cc_start: 0.6096 (OUTLIER) cc_final: 0.5581 (t-90) REVERT: F 151 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7897 (ttm170) REVERT: F 161 MET cc_start: 0.8631 (tpt) cc_final: 0.8404 (tpt) REVERT: F 211 GLU cc_start: 0.9079 (tt0) cc_final: 0.8684 (pt0) REVERT: F 368 ASP cc_start: 0.7956 (m-30) cc_final: 0.7525 (p0) REVERT: I 543 ASN cc_start: 0.7846 (m-40) cc_final: 0.7412 (m110) REVERT: I 624 ASP cc_start: 0.8101 (m-30) cc_final: 0.7774 (m-30) REVERT: I 648 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8149 (pt0) outliers start: 32 outliers final: 22 residues processed: 213 average time/residue: 0.3002 time to fit residues: 91.8430 Evaluate side-chains 219 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 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 660 LEU Chi-restraints excluded: chain E residue 244 THR 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 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 119 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 0.0270 chunk 76 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.138998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106692 restraints weight = 25469.842| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.05 r_work: 0.3345 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15531 Z= 0.114 Angle : 0.604 17.468 21248 Z= 0.288 Chirality : 0.042 0.382 2603 Planarity : 0.003 0.047 2593 Dihedral : 5.337 46.826 3368 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.50 % Allowed : 11.87 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1606 helix: 1.78 (0.27), residues: 407 sheet: 1.01 (0.26), residues: 402 loop : -0.61 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 631 HIS 0.004 0.001 HIS I 585 PHE 0.014 0.001 PHE F 53 TYR 0.012 0.001 TYR I 638 ARG 0.012 0.000 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 46) link_NAG-ASN : angle 1.95165 ( 138) link_BETA1-4 : bond 0.01028 ( 17) link_BETA1-4 : angle 2.88800 ( 51) link_ALPHA1-3 : bond 0.00946 ( 4) link_ALPHA1-3 : angle 1.42827 ( 12) hydrogen bonds : bond 0.03808 ( 468) hydrogen bonds : angle 4.42337 ( 1272) SS BOND : bond 0.00281 ( 33) SS BOND : angle 1.25798 ( 66) covalent geometry : bond 0.00255 (15431) covalent geometry : angle 0.56418 (20981) ********************** 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 223 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.5307 (m) cc_final: 0.5101 (t) REVERT: A 69 TRP cc_start: 0.6507 (m-90) cc_final: 0.5956 (m-90) REVERT: A 94 ASN cc_start: 0.8928 (t0) cc_final: 0.8682 (t0) REVERT: A 106 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7340 (tt0) REVERT: A 207 LYS cc_start: 0.7372 (tmtt) cc_final: 0.6974 (tmtt) REVERT: A 349 LEU cc_start: 0.8489 (mp) cc_final: 0.8148 (mp) REVERT: A 475 MET cc_start: 0.8025 (mmm) cc_final: 0.7347 (mmm) REVERT: A 502 LYS cc_start: 0.8759 (mttt) cc_final: 0.8214 (ttmt) REVERT: A 503 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.5784 (tpp-160) REVERT: B 522 PHE cc_start: 0.8139 (t80) cc_final: 0.7558 (t80) REVERT: B 543 ASN cc_start: 0.8048 (m-40) cc_final: 0.7344 (m-40) REVERT: B 591 GLN cc_start: 0.8014 (tt0) cc_final: 0.7380 (tp40) REVERT: E 51 THR cc_start: 0.9049 (m) cc_final: 0.8658 (p) REVERT: E 82 GLN cc_start: 0.7817 (pp30) cc_final: 0.7369 (pp30) REVERT: E 103 GLN cc_start: 0.7810 (tt0) cc_final: 0.7433 (tm-30) REVERT: E 232 LYS cc_start: 0.8244 (mttt) cc_final: 0.7221 (tptt) REVERT: E 325 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.7213 (t-90) REVERT: G 530 MET cc_start: 0.8046 (tpp) cc_final: 0.7745 (mtt) REVERT: G 590 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.6928 (mp10) REVERT: F 66 HIS cc_start: 0.6090 (OUTLIER) cc_final: 0.5595 (t-90) REVERT: F 151 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7790 (ttm170) REVERT: F 161 MET cc_start: 0.8581 (tpt) cc_final: 0.8334 (tpt) REVERT: F 211 GLU cc_start: 0.9038 (tt0) cc_final: 0.8677 (pt0) REVERT: F 368 ASP cc_start: 0.7966 (m-30) cc_final: 0.7589 (p0) REVERT: I 543 ASN cc_start: 0.7831 (m-40) cc_final: 0.7389 (m110) REVERT: I 624 ASP cc_start: 0.8087 (m-30) cc_final: 0.7773 (m-30) REVERT: I 648 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8115 (pt0) outliers start: 22 outliers final: 13 residues processed: 216 average time/residue: 0.2974 time to fit residues: 93.1344 Evaluate side-chains 209 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 352 HIS 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 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 F residue 66 HIS Chi-restraints excluded: chain F residue 151 ARG 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 165 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN G 651 ASN F 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.138573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106245 restraints weight = 25446.006| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.05 r_work: 0.3340 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4290 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= 0.125 Angle : 0.606 17.354 21248 Z= 0.290 Chirality : 0.042 0.384 2603 Planarity : 0.003 0.046 2593 Dihedral : 5.229 47.235 3368 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.50 % Allowed : 12.07 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1606 helix: 1.83 (0.27), residues: 407 sheet: 1.02 (0.26), residues: 402 loop : -0.60 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 631 HIS 0.003 0.001 HIS I 585 PHE 0.014 0.001 PHE F 53 TYR 0.013 0.001 TYR I 638 ARG 0.010 0.000 ARG I 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 46) link_NAG-ASN : angle 1.94195 ( 138) link_BETA1-4 : bond 0.00953 ( 17) link_BETA1-4 : angle 2.88467 ( 51) link_ALPHA1-3 : bond 0.00922 ( 4) link_ALPHA1-3 : angle 1.43582 ( 12) hydrogen bonds : bond 0.03811 ( 468) hydrogen bonds : angle 4.40099 ( 1272) SS BOND : bond 0.00288 ( 33) SS BOND : angle 1.36251 ( 66) covalent geometry : bond 0.00288 (15431) covalent geometry : angle 0.56576 (20981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8170.84 seconds wall clock time: 146 minutes 50.33 seconds (8810.33 seconds total)