Starting phenix.real_space_refine on Tue Dec 31 09:26:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f9g_28942/12_2024/8f9g_28942.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f9g_28942/12_2024/8f9g_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_28942/12_2024/8f9g_28942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f9g_28942/12_2024/8f9g_28942.map" model { file = "/net/cci-nas-00/data/ceres_data/8f9g_28942/12_2024/8f9g_28942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f9g_28942/12_2024/8f9g_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 11.13, per 1000 atoms: 0.73 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: 4.37 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: 1.82 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: 4.82 Time building geometry restraints manager: 5.00 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: 9.030 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: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.110 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.960 ------------------------------------------------------------------------------- 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 15431 Z= 0.392 Angle : 1.036 10.036 20981 Z= 0.567 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 *********************** 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 : 1.480 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: 0.2996 time to fit residues: 167.3506 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 : 1.527 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 15431 Z= 0.256 Angle : 0.661 12.485 20981 Z= 0.332 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 *********************** 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 : 1.574 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6633 (mm-30) REVERT: A 107 ASP cc_start: 0.7650 (m-30) cc_final: 0.7441 (m-30) REVERT: A 209 SER cc_start: 0.8320 (t) cc_final: 0.8076 (p) REVERT: A 340 GLU cc_start: 0.8370 (tt0) cc_final: 0.7784 (tp30) REVERT: A 349 LEU cc_start: 0.8246 (mt) cc_final: 0.8045 (mt) REVERT: A 370 GLU cc_start: 0.7350 (tt0) cc_final: 0.6930 (mt-10) REVERT: A 475 MET cc_start: 0.7473 (mmm) cc_final: 0.6520 (mmm) REVERT: B 522 PHE cc_start: 0.7769 (t80) cc_final: 0.7240 (t80) REVERT: B 543 ASN cc_start: 0.7527 (m-40) cc_final: 0.6860 (m-40) REVERT: B 630 GLN cc_start: 0.8512 (mt0) cc_final: 0.8311 (mp10) REVERT: E 69 TRP cc_start: 0.7202 (m-90) cc_final: 0.6858 (m-90) REVERT: E 87 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7291 (mp0) REVERT: E 103 GLN cc_start: 0.7141 (tt0) cc_final: 0.6726 (tm-30) REVERT: E 154 ILE cc_start: 0.8598 (mt) cc_final: 0.8273 (mt) REVERT: E 199 SER cc_start: 0.8841 (p) cc_final: 0.8389 (m) REVERT: E 232 LYS cc_start: 0.7730 (mttt) cc_final: 0.6982 (tptt) REVERT: E 280 ASN cc_start: 0.8728 (m-40) cc_final: 0.8399 (m-40) REVERT: E 502 LYS cc_start: 0.8396 (pttm) cc_final: 0.7922 (tmtt) REVERT: G 590 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.5871 (mp10) REVERT: G 636 SER cc_start: 0.9116 (t) cc_final: 0.8636 (m) REVERT: F 66 HIS cc_start: 0.5550 (OUTLIER) cc_final: 0.4979 (t-90) REVERT: F 211 GLU cc_start: 0.9054 (tt0) cc_final: 0.8490 (pt0) REVERT: F 327 ARG cc_start: 0.7669 (mtt90) cc_final: 0.6969 (mtp85) REVERT: F 368 ASP cc_start: 0.7903 (m-30) cc_final: 0.7262 (p0) REVERT: I 539 VAL cc_start: 0.7894 (t) cc_final: 0.7394 (t) REVERT: I 543 ASN cc_start: 0.7354 (m-40) cc_final: 0.6741 (m110) REVERT: I 607 ASN cc_start: 0.8338 (m-40) cc_final: 0.7831 (m-40) REVERT: I 624 ASP cc_start: 0.8178 (m-30) cc_final: 0.7727 (m-30) REVERT: I 636 SER cc_start: 0.8146 (t) cc_final: 0.7844 (m) REVERT: I 648 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8105 (pt0) outliers start: 28 outliers final: 13 residues processed: 256 average time/residue: 0.2802 time to fit residues: 105.4229 Evaluate side-chains 222 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 180 optimal weight: 30.0000 chunk 149 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 249 HIS G 616 ASN G 653 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15431 Z= 0.201 Angle : 0.584 9.935 20981 Z= 0.292 Chirality : 0.043 0.405 2603 Planarity : 0.003 0.040 2593 Dihedral : 7.018 51.753 3368 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.39 % Allowed : 8.19 % Favored : 89.43 % 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: 1.07 (0.21), residues: 1606 helix: 1.49 (0.26), residues: 452 sheet: 1.08 (0.24), residues: 447 loop : 0.04 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 479 HIS 0.003 0.001 HIS F 85 PHE 0.024 0.002 PHE F 53 TYR 0.010 0.001 TYR E 39 ARG 0.005 0.001 ARG I 617 *********************** 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 265 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 1.634 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7582 (m-30) cc_final: 0.7340 (m-30) REVERT: A 209 SER cc_start: 0.8404 (t) cc_final: 0.8195 (p) REVERT: A 340 GLU cc_start: 0.8257 (tt0) cc_final: 0.7939 (tp30) REVERT: A 370 GLU cc_start: 0.7365 (tt0) cc_final: 0.6923 (mt-10) REVERT: A 475 MET cc_start: 0.7417 (mmm) cc_final: 0.6264 (mmm) REVERT: A 503 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.5768 (tpp-160) REVERT: B 522 PHE cc_start: 0.7806 (t80) cc_final: 0.7272 (t80) REVERT: B 543 ASN cc_start: 0.7562 (m-40) cc_final: 0.6884 (m-40) REVERT: B 544 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7282 (mm) REVERT: E 51 THR cc_start: 0.8466 (m) cc_final: 0.8003 (p) REVERT: E 69 TRP cc_start: 0.7180 (m-90) cc_final: 0.6926 (m-90) REVERT: E 103 GLN cc_start: 0.7112 (tt0) cc_final: 0.6706 (tm-30) REVERT: E 199 SER cc_start: 0.8909 (p) cc_final: 0.8298 (m) REVERT: E 232 LYS cc_start: 0.7799 (mttt) cc_final: 0.6949 (tptt) REVERT: E 280 ASN cc_start: 0.8696 (m-40) cc_final: 0.8352 (m-40) REVERT: E 502 LYS cc_start: 0.8353 (pttm) cc_final: 0.7984 (tmtt) REVERT: G 590 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.5742 (mp10) REVERT: F 66 HIS cc_start: 0.5606 (OUTLIER) cc_final: 0.5038 (t-90) REVERT: F 161 MET cc_start: 0.8135 (tpt) cc_final: 0.7601 (tpt) REVERT: F 211 GLU cc_start: 0.9040 (tt0) cc_final: 0.8484 (pt0) REVERT: F 368 ASP cc_start: 0.7878 (m-30) cc_final: 0.7261 (p0) REVERT: I 539 VAL cc_start: 0.7759 (t) cc_final: 0.7218 (t) REVERT: I 543 ASN cc_start: 0.7368 (m-40) cc_final: 0.6785 (m110) REVERT: I 607 ASN cc_start: 0.8399 (m-40) cc_final: 0.7874 (m-40) REVERT: I 624 ASP cc_start: 0.8101 (m-30) cc_final: 0.7781 (m-30) REVERT: I 636 SER cc_start: 0.8440 (t) cc_final: 0.8147 (m) REVERT: I 648 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8039 (pt0) outliers start: 35 outliers final: 20 residues processed: 249 average time/residue: 0.2798 time to fit residues: 101.5966 Evaluate side-chains 236 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 264 SER 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 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 165 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 177 optimal weight: 30.0000 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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 F 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15431 Z= 0.299 Angle : 0.626 11.071 20981 Z= 0.312 Chirality : 0.044 0.409 2603 Planarity : 0.004 0.039 2593 Dihedral : 6.463 56.111 3368 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.93 % Allowed : 7.98 % Favored : 89.09 % 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: 0.93 (0.21), residues: 1606 helix: 1.50 (0.26), residues: 436 sheet: 1.28 (0.24), residues: 423 loop : -0.28 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 479 HIS 0.006 0.001 HIS F 85 PHE 0.027 0.002 PHE F 53 TYR 0.012 0.001 TYR I 638 ARG 0.006 0.001 ARG I 617 *********************** 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 254 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8491 (t0) cc_final: 0.8049 (t0) REVERT: A 209 SER cc_start: 0.8469 (t) cc_final: 0.8255 (p) REVERT: A 340 GLU cc_start: 0.8240 (tt0) cc_final: 0.7964 (tp30) REVERT: A 349 LEU cc_start: 0.8227 (mt) cc_final: 0.8015 (mp) REVERT: A 370 GLU cc_start: 0.7456 (tt0) cc_final: 0.6980 (mt-10) REVERT: A 425 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7487 (t0) REVERT: A 502 LYS cc_start: 0.8606 (mttt) cc_final: 0.7959 (ttmt) REVERT: A 503 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.5651 (tpp-160) REVERT: B 522 PHE cc_start: 0.7846 (t80) cc_final: 0.7113 (t80) REVERT: B 543 ASN cc_start: 0.7565 (m-40) cc_final: 0.6789 (m-40) REVERT: B 591 GLN cc_start: 0.7455 (tt0) cc_final: 0.6862 (tp40) REVERT: E 51 THR cc_start: 0.8518 (m) cc_final: 0.8067 (p) REVERT: E 103 GLN cc_start: 0.7196 (tt0) cc_final: 0.6789 (tm-30) REVERT: E 232 LYS cc_start: 0.8023 (mttt) cc_final: 0.7075 (tptt) REVERT: E 280 ASN cc_start: 0.8743 (m-40) cc_final: 0.8383 (m-40) REVERT: E 502 LYS cc_start: 0.8370 (pttm) cc_final: 0.8046 (tmtt) REVERT: G 590 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.5915 (mp10) REVERT: G 648 GLU cc_start: 0.8296 (tp30) cc_final: 0.8040 (tp30) REVERT: F 125 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7844 (mt) REVERT: F 151 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7168 (ttm170) REVERT: F 161 MET cc_start: 0.8147 (tpt) cc_final: 0.7795 (tpt) REVERT: F 211 GLU cc_start: 0.9060 (tt0) cc_final: 0.8501 (pt0) REVERT: F 368 ASP cc_start: 0.7855 (m-30) cc_final: 0.7242 (p0) REVERT: I 539 VAL cc_start: 0.7699 (t) cc_final: 0.7226 (t) REVERT: I 543 ASN cc_start: 0.7447 (m-40) cc_final: 0.6875 (m110) REVERT: I 607 ASN cc_start: 0.8415 (m-40) cc_final: 0.8099 (m-40) REVERT: I 621 GLU cc_start: 0.7621 (tp30) cc_final: 0.7336 (tp30) REVERT: I 624 ASP cc_start: 0.8045 (m-30) cc_final: 0.7721 (m-30) REVERT: I 626 MET cc_start: 0.7471 (mtt) cc_final: 0.7186 (mtt) REVERT: I 636 SER cc_start: 0.8472 (t) cc_final: 0.8168 (m) REVERT: I 648 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8004 (pt0) outliers start: 43 outliers final: 27 residues processed: 234 average time/residue: 0.3027 time to fit residues: 102.8257 Evaluate side-chains 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 371 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 587 LEU Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 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 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 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 148 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN B 653 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15431 Z= 0.342 Angle : 0.631 11.377 20981 Z= 0.315 Chirality : 0.044 0.411 2603 Planarity : 0.004 0.049 2593 Dihedral : 6.387 59.054 3368 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.73 % Allowed : 8.39 % 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: 0.80 (0.21), residues: 1606 helix: 1.75 (0.27), residues: 412 sheet: 1.09 (0.25), residues: 423 loop : -0.45 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 69 HIS 0.006 0.001 HIS F 374 PHE 0.023 0.002 PHE F 53 TYR 0.013 0.002 TYR E 217 ARG 0.006 0.001 ARG I 617 *********************** 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 244 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8458 (t) cc_final: 0.8230 (p) REVERT: A 340 GLU cc_start: 0.8220 (tt0) cc_final: 0.7945 (tp30) REVERT: A 349 LEU cc_start: 0.8298 (mt) cc_final: 0.8056 (mp) REVERT: A 370 GLU cc_start: 0.7505 (tt0) cc_final: 0.6985 (mt-10) REVERT: A 425 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7418 (t0) REVERT: A 475 MET cc_start: 0.7552 (mmm) cc_final: 0.6366 (mmm) REVERT: A 502 LYS cc_start: 0.8633 (mttt) cc_final: 0.7993 (ttmt) REVERT: A 503 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.5602 (tpp-160) REVERT: B 522 PHE cc_start: 0.7807 (t80) cc_final: 0.6944 (t80) REVERT: B 544 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7444 (mm) REVERT: B 591 GLN cc_start: 0.7566 (tt0) cc_final: 0.7063 (tp40) REVERT: E 51 THR cc_start: 0.8547 (m) cc_final: 0.8125 (p) REVERT: E 82 GLN cc_start: 0.7450 (pp30) cc_final: 0.7045 (pp30) REVERT: E 103 GLN cc_start: 0.7168 (tt0) cc_final: 0.6748 (tm-30) REVERT: E 232 LYS cc_start: 0.8150 (mttt) cc_final: 0.7175 (tptt) REVERT: E 325 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7018 (t-90) REVERT: E 502 LYS cc_start: 0.8401 (pttm) cc_final: 0.7995 (tmtt) REVERT: G 590 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.5974 (mp10) REVERT: G 648 GLU cc_start: 0.8331 (tp30) cc_final: 0.8105 (tp30) REVERT: F 66 HIS cc_start: 0.5550 (OUTLIER) cc_final: 0.4992 (t-90) REVERT: F 151 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7095 (ttm170) REVERT: F 211 GLU cc_start: 0.9060 (tt0) cc_final: 0.8497 (pt0) REVERT: F 368 ASP cc_start: 0.7837 (m-30) cc_final: 0.7221 (p0) REVERT: F 502 LYS cc_start: 0.8629 (mttt) cc_final: 0.8216 (tmtt) REVERT: I 543 ASN cc_start: 0.7401 (m-40) cc_final: 0.6878 (m-40) REVERT: I 601 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7953 (mtpp) REVERT: I 607 ASN cc_start: 0.8440 (m-40) cc_final: 0.8224 (m-40) REVERT: I 624 ASP cc_start: 0.8058 (m-30) cc_final: 0.7691 (m-30) REVERT: I 626 MET cc_start: 0.7298 (mtt) cc_final: 0.7055 (mtt) REVERT: I 636 SER cc_start: 0.8477 (t) cc_final: 0.8271 (m) REVERT: I 648 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8030 (pt0) outliers start: 40 outliers final: 25 residues processed: 228 average time/residue: 0.2989 time to fit residues: 98.7895 Evaluate side-chains 232 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 1.637 ------------------------------------------------------------------------------- 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 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 630 GLN 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 371 VAL 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 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 59 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 178 optimal weight: 30.0000 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15431 Z= 0.212 Angle : 0.567 10.681 20981 Z= 0.282 Chirality : 0.042 0.395 2603 Planarity : 0.003 0.059 2593 Dihedral : 6.042 59.739 3368 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.25 % Allowed : 9.14 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.21), residues: 1606 helix: 1.86 (0.27), residues: 412 sheet: 1.04 (0.25), residues: 423 loop : -0.49 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 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 *********************** 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 244 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.4845 (m) cc_final: 0.4524 (t) REVERT: A 94 ASN cc_start: 0.8521 (t0) cc_final: 0.8125 (t0) REVERT: A 106 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6542 (tt0) REVERT: A 209 SER cc_start: 0.8477 (t) cc_final: 0.8132 (p) REVERT: A 340 GLU cc_start: 0.8159 (tt0) cc_final: 0.7875 (tp30) REVERT: A 349 LEU cc_start: 0.8215 (mt) cc_final: 0.8007 (mt) REVERT: A 370 GLU cc_start: 0.7474 (tt0) cc_final: 0.6973 (mt-10) REVERT: A 475 MET cc_start: 0.7444 (mmm) cc_final: 0.6393 (mmm) REVERT: A 502 LYS cc_start: 0.8623 (mttt) cc_final: 0.7959 (ttmt) REVERT: A 503 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.5506 (tpp-160) REVERT: B 522 PHE cc_start: 0.7761 (t80) cc_final: 0.6928 (t80) REVERT: B 543 ASN cc_start: 0.7594 (m-40) cc_final: 0.6713 (m-40) REVERT: B 544 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7459 (mm) REVERT: B 591 GLN cc_start: 0.7462 (tt0) cc_final: 0.6863 (tp40) REVERT: B 654 GLU cc_start: 0.8010 (tp30) cc_final: 0.7727 (tp30) REVERT: E 51 THR cc_start: 0.8544 (m) cc_final: 0.8113 (p) REVERT: E 82 GLN cc_start: 0.7569 (pp30) cc_final: 0.7157 (pp30) REVERT: E 103 GLN cc_start: 0.7106 (tt0) cc_final: 0.6695 (tm-30) REVERT: E 232 LYS cc_start: 0.8119 (mttt) cc_final: 0.7114 (tptt) REVERT: E 280 ASN cc_start: 0.8724 (m-40) cc_final: 0.8331 (m-40) REVERT: E 325 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7013 (t-90) REVERT: E 502 LYS cc_start: 0.8389 (pttm) cc_final: 0.8001 (tmtt) REVERT: G 590 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.5941 (mp10) REVERT: G 648 GLU cc_start: 0.8350 (tp30) cc_final: 0.8102 (tp30) REVERT: F 66 HIS cc_start: 0.5533 (OUTLIER) cc_final: 0.4985 (t-90) REVERT: F 151 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7133 (ttm170) REVERT: F 161 MET cc_start: 0.8137 (tpt) cc_final: 0.7799 (tpt) REVERT: F 211 GLU cc_start: 0.9039 (tt0) cc_final: 0.8508 (pt0) REVERT: F 368 ASP cc_start: 0.7829 (m-30) cc_final: 0.7235 (p0) REVERT: F 502 LYS cc_start: 0.8570 (mttt) cc_final: 0.8176 (tmtt) REVERT: I 543 ASN cc_start: 0.7386 (m-40) cc_final: 0.6880 (m-40) REVERT: I 607 ASN cc_start: 0.8414 (m-40) cc_final: 0.8203 (m-40) REVERT: I 624 ASP cc_start: 0.8006 (m-30) cc_final: 0.7622 (m-30) REVERT: I 626 MET cc_start: 0.7267 (mtt) cc_final: 0.6996 (mtt) REVERT: I 648 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8024 (pt0) outliers start: 33 outliers final: 23 residues processed: 232 average time/residue: 0.2924 time to fit residues: 98.5851 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 : 1.608 ------------------------------------------------------------------------------- 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 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 630 GLN Chi-restraints excluded: chain B residue 648 GLU 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 535 MET Chi-restraints excluded: chain G residue 587 LEU Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 30.0000 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 585 HIS B 630 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15431 Z= 0.352 Angle : 0.632 11.548 20981 Z= 0.314 Chirality : 0.045 0.408 2603 Planarity : 0.004 0.049 2593 Dihedral : 6.184 53.043 3368 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.59 % Allowed : 9.41 % Favored : 87.99 % 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: 0.55 (0.21), residues: 1606 helix: 1.74 (0.27), residues: 412 sheet: 0.86 (0.25), residues: 423 loop : -0.68 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 631 HIS 0.005 0.001 HIS F 85 PHE 0.019 0.002 PHE F 53 TYR 0.016 0.002 TYR E 217 ARG 0.006 0.001 ARG I 617 *********************** 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 242 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6104 (m-90) cc_final: 0.5280 (m-90) REVERT: A 94 ASN cc_start: 0.8557 (t0) cc_final: 0.8142 (t0) REVERT: A 209 SER cc_start: 0.8561 (t) cc_final: 0.8350 (p) REVERT: A 340 GLU cc_start: 0.8211 (tt0) cc_final: 0.7956 (tp30) REVERT: A 370 GLU cc_start: 0.7397 (tt0) cc_final: 0.6870 (mt-10) REVERT: A 425 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7424 (t0) REVERT: A 475 MET cc_start: 0.7574 (mmm) cc_final: 0.6338 (mmm) REVERT: A 502 LYS cc_start: 0.8701 (mttt) cc_final: 0.8083 (ttmt) REVERT: A 503 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.5535 (tpp-160) REVERT: B 522 PHE cc_start: 0.7800 (t80) cc_final: 0.7041 (t80) REVERT: B 543 ASN cc_start: 0.7518 (m-40) cc_final: 0.6666 (m-40) REVERT: B 544 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7565 (mm) REVERT: B 591 GLN cc_start: 0.7539 (tt0) cc_final: 0.7080 (tp40) REVERT: E 51 THR cc_start: 0.8581 (m) cc_final: 0.8192 (p) REVERT: E 82 GLN cc_start: 0.7536 (pp30) cc_final: 0.7122 (pp30) REVERT: E 103 GLN cc_start: 0.7119 (tt0) cc_final: 0.6708 (tm-30) REVERT: E 232 LYS cc_start: 0.8236 (mttt) cc_final: 0.7144 (tptt) REVERT: E 325 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7049 (t-90) REVERT: E 502 LYS cc_start: 0.8377 (pttm) cc_final: 0.7967 (tmtt) REVERT: G 530 MET cc_start: 0.7324 (mtp) cc_final: 0.6786 (mtt) REVERT: G 535 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8542 (ttm) REVERT: G 590 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.5955 (mp10) REVERT: G 648 GLU cc_start: 0.8311 (tp30) cc_final: 0.8049 (tp30) REVERT: F 66 HIS cc_start: 0.5587 (OUTLIER) cc_final: 0.5025 (t-90) REVERT: F 151 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7241 (ttm170) REVERT: F 161 MET cc_start: 0.8189 (tpt) cc_final: 0.7899 (tpt) REVERT: F 211 GLU cc_start: 0.9070 (tt0) cc_final: 0.8537 (pt0) REVERT: F 368 ASP cc_start: 0.7739 (m-30) cc_final: 0.7135 (p0) REVERT: F 475 MET cc_start: 0.7897 (mmt) cc_final: 0.7626 (mmt) REVERT: F 502 LYS cc_start: 0.8687 (mttt) cc_final: 0.8294 (tmtt) REVERT: I 543 ASN cc_start: 0.7363 (m-40) cc_final: 0.6873 (m-40) REVERT: I 607 ASN cc_start: 0.8351 (m-40) cc_final: 0.8141 (m-40) REVERT: I 624 ASP cc_start: 0.7978 (m-30) cc_final: 0.7606 (m-30) REVERT: I 626 MET cc_start: 0.7224 (mtt) cc_final: 0.7001 (mtt) REVERT: I 648 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8015 (pt0) outliers start: 38 outliers final: 24 residues processed: 226 average time/residue: 0.2932 time to fit residues: 96.1406 Evaluate side-chains 230 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.672 ------------------------------------------------------------------------------- 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 357 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 434 MET 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 630 GLN 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 378 CYS 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 151 ARG 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 109 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN B 653 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15431 Z= 0.269 Angle : 0.597 11.145 20981 Z= 0.296 Chirality : 0.043 0.394 2603 Planarity : 0.003 0.056 2593 Dihedral : 6.015 59.734 3368 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.32 % Allowed : 10.03 % 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: 0.58 (0.21), residues: 1606 helix: 2.02 (0.27), residues: 394 sheet: 0.84 (0.25), residues: 417 loop : -0.71 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 631 HIS 0.004 0.001 HIS F 216 PHE 0.016 0.002 PHE F 53 TYR 0.013 0.001 TYR E 217 ARG 0.007 0.000 ARG I 617 *********************** 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 240 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.4977 (m) cc_final: 0.4349 (t) REVERT: A 69 TRP cc_start: 0.6079 (m-90) cc_final: 0.5297 (m-90) REVERT: A 94 ASN cc_start: 0.8549 (t0) cc_final: 0.8140 (t0) REVERT: A 207 LYS cc_start: 0.7985 (pttt) cc_final: 0.7749 (tmtt) REVERT: A 209 SER cc_start: 0.8537 (t) cc_final: 0.8320 (p) REVERT: A 340 GLU cc_start: 0.8176 (tt0) cc_final: 0.7913 (tp30) REVERT: A 349 LEU cc_start: 0.8334 (mt) cc_final: 0.8079 (mt) REVERT: A 370 GLU cc_start: 0.7466 (tt0) cc_final: 0.6924 (mt-10) REVERT: A 475 MET cc_start: 0.7541 (mmm) cc_final: 0.6388 (mmm) REVERT: A 502 LYS cc_start: 0.8687 (mttt) cc_final: 0.8046 (ttmt) REVERT: A 503 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.5530 (tpp-160) REVERT: B 522 PHE cc_start: 0.7785 (t80) cc_final: 0.7015 (t80) REVERT: B 543 ASN cc_start: 0.7517 (m-40) cc_final: 0.6739 (m-40) REVERT: B 544 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7602 (mm) REVERT: B 591 GLN cc_start: 0.7509 (tt0) cc_final: 0.6903 (tp40) REVERT: E 51 THR cc_start: 0.8576 (m) cc_final: 0.8208 (p) REVERT: E 82 GLN cc_start: 0.7396 (pp30) cc_final: 0.6981 (pp30) REVERT: E 103 GLN cc_start: 0.7061 (tt0) cc_final: 0.6653 (tm-30) REVERT: E 232 LYS cc_start: 0.8249 (mttt) cc_final: 0.7093 (tptt) REVERT: E 325 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7080 (t-90) REVERT: E 502 LYS cc_start: 0.8398 (pttm) cc_final: 0.7981 (tmtt) REVERT: G 530 MET cc_start: 0.7290 (mtp) cc_final: 0.6889 (mtt) REVERT: G 590 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.5999 (mp10) REVERT: G 648 GLU cc_start: 0.8319 (tp30) cc_final: 0.8044 (tp30) REVERT: F 66 HIS cc_start: 0.5452 (OUTLIER) cc_final: 0.4930 (t-90) REVERT: F 151 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7253 (ttm170) REVERT: F 161 MET cc_start: 0.8150 (tpt) cc_final: 0.7849 (tpt) REVERT: F 211 GLU cc_start: 0.9073 (tt0) cc_final: 0.8537 (pt0) REVERT: F 368 ASP cc_start: 0.7744 (m-30) cc_final: 0.7145 (p0) REVERT: F 475 MET cc_start: 0.7730 (mmt) cc_final: 0.7455 (mmt) REVERT: F 502 LYS cc_start: 0.8645 (mttt) cc_final: 0.8259 (tttm) REVERT: I 543 ASN cc_start: 0.7281 (m-40) cc_final: 0.6774 (m-40) REVERT: I 624 ASP cc_start: 0.7969 (m-30) cc_final: 0.7601 (m-30) REVERT: I 626 MET cc_start: 0.7184 (mtt) cc_final: 0.6956 (mtt) REVERT: I 648 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8009 (pt0) outliers start: 34 outliers final: 25 residues processed: 225 average time/residue: 0.3004 time to fit residues: 97.7214 Evaluate side-chains 230 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 434 MET 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 630 GLN 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 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain G residue 587 LEU Chi-restraints excluded: chain G residue 590 GLN Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 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 169 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15431 Z= 0.377 Angle : 0.653 13.868 20981 Z= 0.320 Chirality : 0.045 0.406 2603 Planarity : 0.004 0.050 2593 Dihedral : 6.149 53.589 3368 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.39 % Allowed : 9.96 % 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: 0.33 (0.21), residues: 1606 helix: 1.59 (0.27), residues: 412 sheet: 0.55 (0.25), residues: 435 loop : -0.74 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 631 HIS 0.005 0.001 HIS F 216 PHE 0.018 0.002 PHE F 53 TYR 0.017 0.002 TYR E 217 ARG 0.006 0.001 ARG I 617 *********************** 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 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6122 (m-90) cc_final: 0.5339 (m-90) REVERT: A 94 ASN cc_start: 0.8577 (t0) cc_final: 0.8159 (t0) REVERT: A 207 LYS cc_start: 0.7992 (pttt) cc_final: 0.7791 (tmtt) REVERT: A 209 SER cc_start: 0.8512 (t) cc_final: 0.8271 (p) REVERT: A 340 GLU cc_start: 0.8208 (tt0) cc_final: 0.7978 (tp30) REVERT: A 370 GLU cc_start: 0.7410 (tt0) cc_final: 0.6869 (mt-10) REVERT: A 475 MET cc_start: 0.7584 (mmm) cc_final: 0.6318 (mmm) REVERT: A 502 LYS cc_start: 0.8670 (mttt) cc_final: 0.8066 (ttmt) REVERT: A 503 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.5561 (tpp-160) REVERT: B 522 PHE cc_start: 0.7804 (t80) cc_final: 0.7077 (t80) REVERT: B 543 ASN cc_start: 0.7553 (m-40) cc_final: 0.6735 (m-40) REVERT: B 544 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7626 (mm) REVERT: B 591 GLN cc_start: 0.7602 (tt0) cc_final: 0.6970 (tp40) REVERT: E 51 THR cc_start: 0.8586 (m) cc_final: 0.8245 (p) REVERT: E 82 GLN cc_start: 0.7403 (pp30) cc_final: 0.6991 (pp30) REVERT: E 103 GLN cc_start: 0.7119 (tt0) cc_final: 0.6717 (tm-30) REVERT: E 232 LYS cc_start: 0.8273 (mttt) cc_final: 0.7145 (tptt) REVERT: E 325 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.7095 (t-90) REVERT: E 502 LYS cc_start: 0.8384 (pttm) cc_final: 0.7957 (tmtt) REVERT: G 530 MET cc_start: 0.7335 (mtp) cc_final: 0.7101 (mtt) REVERT: G 590 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6038 (mp10) REVERT: G 648 GLU cc_start: 0.8323 (tp30) cc_final: 0.8058 (tp30) REVERT: F 66 HIS cc_start: 0.5470 (OUTLIER) cc_final: 0.4931 (t-90) REVERT: F 151 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7366 (ttm170) REVERT: F 161 MET cc_start: 0.8197 (tpt) cc_final: 0.7870 (tpt) REVERT: F 211 GLU cc_start: 0.9047 (tt0) cc_final: 0.8479 (pt0) REVERT: F 368 ASP cc_start: 0.7741 (m-30) cc_final: 0.7112 (p0) REVERT: F 475 MET cc_start: 0.7722 (mmt) cc_final: 0.7471 (mmt) REVERT: F 502 LYS cc_start: 0.8644 (mttt) cc_final: 0.8371 (tttm) REVERT: I 543 ASN cc_start: 0.7316 (m-40) cc_final: 0.6800 (m110) REVERT: I 624 ASP cc_start: 0.7959 (m-30) cc_final: 0.7602 (m-30) REVERT: I 626 MET cc_start: 0.7180 (mtt) cc_final: 0.6963 (mtt) REVERT: I 648 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8012 (pt0) outliers start: 35 outliers final: 23 residues processed: 220 average time/residue: 0.3077 time to fit residues: 97.3298 Evaluate side-chains 223 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 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 194 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 40.0000 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 0.0770 chunk 183 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 145 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN B 653 GLN E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN F 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15431 Z= 0.180 Angle : 0.564 13.384 20981 Z= 0.279 Chirality : 0.043 0.386 2603 Planarity : 0.003 0.052 2593 Dihedral : 5.604 48.495 3368 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.77 % Allowed : 10.85 % Favored : 87.38 % 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: 1.78 (0.27), residues: 407 sheet: 0.79 (0.25), residues: 417 loop : -0.70 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP I 631 HIS 0.003 0.001 HIS I 585 PHE 0.014 0.001 PHE F 53 TYR 0.016 0.001 TYR E 40 ARG 0.007 0.000 ARG I 617 ********************** 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 233 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.4789 (m) cc_final: 0.4362 (t) REVERT: A 94 ASN cc_start: 0.8558 (t0) cc_final: 0.8145 (t0) REVERT: A 106 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6567 (tt0) REVERT: A 209 SER cc_start: 0.8505 (t) cc_final: 0.8254 (p) REVERT: A 246 GLN cc_start: 0.6009 (mp10) cc_final: 0.5775 (pm20) REVERT: A 340 GLU cc_start: 0.8111 (tt0) cc_final: 0.7847 (tp30) REVERT: A 349 LEU cc_start: 0.8256 (mt) cc_final: 0.8029 (mt) REVERT: A 370 GLU cc_start: 0.7402 (tt0) cc_final: 0.6873 (mt-10) REVERT: A 475 MET cc_start: 0.7425 (mmm) cc_final: 0.6468 (mmm) REVERT: A 502 LYS cc_start: 0.8637 (mttt) cc_final: 0.8026 (tttt) REVERT: A 503 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.5591 (tpp-160) REVERT: B 522 PHE cc_start: 0.7759 (t80) cc_final: 0.7089 (t80) REVERT: B 543 ASN cc_start: 0.7540 (m-40) cc_final: 0.6792 (m-40) REVERT: B 591 GLN cc_start: 0.7430 (tt0) cc_final: 0.6859 (tp40) REVERT: E 51 THR cc_start: 0.8565 (m) cc_final: 0.8203 (p) REVERT: E 82 GLN cc_start: 0.7445 (pp30) cc_final: 0.7094 (pp30) REVERT: E 103 GLN cc_start: 0.6997 (tt0) cc_final: 0.6609 (tm-30) REVERT: E 232 LYS cc_start: 0.8223 (mttt) cc_final: 0.7054 (tptt) REVERT: E 325 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7115 (t-90) REVERT: E 502 LYS cc_start: 0.8347 (pttm) cc_final: 0.7905 (tmtt) REVERT: G 530 MET cc_start: 0.7271 (mtp) cc_final: 0.6937 (mtt) REVERT: G 590 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6031 (mp10) REVERT: G 648 GLU cc_start: 0.8308 (tp30) cc_final: 0.8037 (tp30) REVERT: F 66 HIS cc_start: 0.5471 (OUTLIER) cc_final: 0.4959 (t-90) REVERT: F 151 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7299 (ttm170) REVERT: F 161 MET cc_start: 0.8090 (tpt) cc_final: 0.7776 (tpt) REVERT: F 211 GLU cc_start: 0.9067 (tt0) cc_final: 0.8513 (pt0) REVERT: F 368 ASP cc_start: 0.7764 (m-30) cc_final: 0.7168 (p0) REVERT: F 475 MET cc_start: 0.7751 (mmt) cc_final: 0.7095 (mmm) REVERT: F 502 LYS cc_start: 0.8592 (mttt) cc_final: 0.8249 (tttm) REVERT: I 543 ASN cc_start: 0.7314 (m-40) cc_final: 0.6739 (m110) REVERT: I 624 ASP cc_start: 0.7976 (m-30) cc_final: 0.7634 (m-30) REVERT: I 648 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7986 (pt0) outliers start: 26 outliers final: 17 residues processed: 224 average time/residue: 0.2980 time to fit residues: 97.0464 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 : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 195 ASN 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 595 ILE 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 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 155 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 128 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 651 ASN F 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.138029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105823 restraints weight = 25154.879| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.05 r_work: 0.3322 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.290 15431 Z= 0.299 Angle : 0.863 59.192 20981 Z= 0.515 Chirality : 0.050 1.052 2603 Planarity : 0.004 0.112 2593 Dihedral : 5.630 48.416 3368 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.68 % Favored : 97.20 % Rotamer: Outliers : 1.77 % Allowed : 11.19 % Favored : 87.04 % Cbeta Deviations : 0.11 % 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: 0.47 (0.21), residues: 1606 helix: 1.73 (0.27), residues: 407 sheet: 0.79 (0.25), residues: 417 loop : -0.73 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 631 HIS 0.003 0.001 HIS A 66 PHE 0.014 0.001 PHE A 53 TYR 0.012 0.001 TYR E 40 ARG 0.011 0.000 ARG I 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3393.06 seconds wall clock time: 63 minutes 58.50 seconds (3838.50 seconds total)