Starting phenix.real_space_refine on Sun Aug 24 12:32:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8san_40274/08_2025/8san_40274_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8san_40274/08_2025/8san_40274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8san_40274/08_2025/8san_40274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8san_40274/08_2025/8san_40274.map" model { file = "/net/cci-nas-00/data/ceres_data/8san_40274/08_2025/8san_40274_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8san_40274/08_2025/8san_40274_neut.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 135 5.16 5 C 12486 2.51 5 N 3402 2.21 5 O 3885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19908 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3538 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain breaks: 1 Chain: "B" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1154 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "E" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3538 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain breaks: 1 Chain: "F" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1154 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "I" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3538 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain breaks: 1 Chain: "J" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1154 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.45, per 1000 atoms: 0.22 Number of scatterers: 19908 At special positions: 0 Unit cell: (140.712, 148.174, 121.524, 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 135 16.00 O 3885 8.00 N 3402 7.00 C 12486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 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 F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 86 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 86 " 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 N 3 " - " MAN N 7 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 7 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 7 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 6 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 6 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 6 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 6 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN E 197 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 276 " " NAG S 1 " - " ASN I 197 " " NAG T 1 " - " ASN I 262 " " NAG U 1 " - " ASN I 276 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 637.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 52 sheets defined 21.7% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.714A pdb=" N TRP A 35 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL A 36 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.262A pdb=" N LYS A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.799A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 removed outlier: 4.171A pdb=" N ASN A 392 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.952A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.996A pdb=" N ALA B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.127A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 569 through 595 removed outlier: 3.968A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.381A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.748A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.564A pdb=" N ASP C 31 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 59 through 64 removed outlier: 3.906A pdb=" N LYS E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS E 63 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.873A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.129A pdb=" N ASN E 392 " --> pdb=" O LYS E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 479 Processing helix chain 'F' and resid 521 through 526 Processing helix chain 'F' and resid 529 through 535 Processing helix chain 'F' and resid 536 through 538 No H-bonds generated for 'chain 'F' and resid 536 through 538' Processing helix chain 'F' and resid 539 through 546 removed outlier: 3.560A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 567 Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.593A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 631 removed outlier: 3.526A pdb=" N GLN F 630 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.687A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 31 through 35 Processing helix chain 'I' and resid 59 through 64 removed outlier: 4.038A pdb=" N LYS I 62 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS I 63 " --> pdb=" O ALA I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.584A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 181 Processing helix chain 'I' and resid 335 through 351 removed outlier: 3.598A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.201A pdb=" N ASN I 392 " --> pdb=" O LYS I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.950A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 525 Processing helix chain 'J' and resid 529 through 535 removed outlier: 3.644A pdb=" N MET J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 538 No H-bonds generated for 'chain 'J' and resid 536 through 538' Processing helix chain 'J' and resid 539 through 544 removed outlier: 3.521A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 567 removed outlier: 3.565A pdb=" N LEU J 565 " --> pdb=" O ALA J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 595 Processing helix chain 'J' and resid 619 through 625 Processing helix chain 'J' and resid 627 through 630 Processing helix chain 'J' and resid 631 through 636 removed outlier: 4.336A pdb=" N ILE J 635 " --> pdb=" O TRP J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.726A pdb=" N ASP K 31 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.939A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.882A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.529A pdb=" N LYS A 170 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.823A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 434 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.489A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.567A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 385 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 271 removed outlier: 11.192A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.567A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 304 removed outlier: 7.301A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 360 removed outlier: 6.434A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.541A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 72 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.595A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 35 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 37 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 91 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.595A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 35 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 37 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 91 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.523A pdb=" N THR D 5 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR D 69 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 72 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER D 61 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.810A pdb=" N LEU D 11 " --> pdb=" O GLN D 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 32 through 34 Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.955A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.804A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 129 through 131 removed outlier: 3.887A pdb=" N ILE E 130 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.767A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.625A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.524A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.547A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.815A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.060A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 270 through 274 removed outlier: 3.591A pdb=" N ARG E 273 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 285 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.060A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.815A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.547A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.524A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 301 through 304 removed outlier: 7.247A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC8, first strand: chain 'E' and resid 358 through 360 removed outlier: 6.202A pdb=" N THR E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.545A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP G 72 " --> pdb=" O THR G 77 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 56 through 57 removed outlier: 3.540A pdb=" N ALA G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 52 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 35 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 37 " --> pdb=" O PHE G 91 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 56 through 57 removed outlier: 3.540A pdb=" N ALA G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 52 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 35 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 37 " --> pdb=" O PHE G 91 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.394A pdb=" N TYR H 69 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER H 61 " --> pdb=" O THR H 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.021A pdb=" N LEU H 11 " --> pdb=" O GLN H 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 32 through 34 Processing sheet with id=AD6, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AD7, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.907A pdb=" N VAL I 38 " --> pdb=" O CYS J 604 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.542A pdb=" N LEU I 226 " --> pdb=" O LYS I 487 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 54 through 55 removed outlier: 5.913A pdb=" N ILE I 215 " --> pdb=" O GLY I 250 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY I 250 " --> pdb=" O ILE I 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR I 217 " --> pdb=" O THR I 248 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 91 through 92 removed outlier: 3.793A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AE3, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.966A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.564A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS I 378 " --> pdb=" O GLU I 381 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS I 385 " --> pdb=" O HIS I 374 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 270 through 271 removed outlier: 6.585A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 301 through 304 removed outlier: 7.267A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 307 through 308 Processing sheet with id=AE8, first strand: chain 'I' and resid 358 through 360 removed outlier: 6.338A pdb=" N THR I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AF1, first strand: chain 'K' and resid 18 through 20 Processing sheet with id=AF2, first strand: chain 'K' and resid 57 through 59 removed outlier: 4.203A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG K 38 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 57 through 59 removed outlier: 4.203A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG K 38 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.527A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR L 69 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.962A pdb=" N LEU L 11 " --> pdb=" O GLN L 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 32 through 34 Processing sheet with id=AF7, first strand: chain 'L' and resid 46 through 47 577 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6386 1.35 - 1.47: 5097 1.47 - 1.60: 8668 1.60 - 1.73: 3 1.73 - 1.86: 180 Bond restraints: 20334 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.621 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.619 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.613 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C LYS E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.328 1.365 -0.037 1.25e-02 6.40e+03 8.68e+00 bond pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 1.408 1.466 -0.058 2.00e-02 2.50e+03 8.53e+00 ... (remaining 20329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 26438 2.12 - 4.25: 912 4.25 - 6.37: 214 6.37 - 8.50: 29 8.50 - 10.62: 10 Bond angle restraints: 27603 Sorted by residual: angle pdb=" C SER J 613 " pdb=" N TRP J 614 " pdb=" CA TRP J 614 " ideal model delta sigma weight residual 121.70 132.32 -10.62 1.80e+00 3.09e-01 3.48e+01 angle pdb=" C SER F 613 " pdb=" N TRP F 614 " pdb=" CA TRP F 614 " ideal model delta sigma weight residual 121.70 132.28 -10.58 1.80e+00 3.09e-01 3.45e+01 angle pdb=" C SER B 613 " pdb=" N TRP B 614 " pdb=" CA TRP B 614 " ideal model delta sigma weight residual 121.70 132.17 -10.47 1.80e+00 3.09e-01 3.39e+01 angle pdb=" C ARG D 24 " pdb=" N THR D 25 " pdb=" CA THR D 25 " ideal model delta sigma weight residual 121.70 131.07 -9.37 1.80e+00 3.09e-01 2.71e+01 angle pdb=" C ARG H 24 " pdb=" N THR H 25 " pdb=" CA THR H 25 " ideal model delta sigma weight residual 121.70 130.91 -9.21 1.80e+00 3.09e-01 2.62e+01 ... (remaining 27598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 12040 23.68 - 47.35: 628 47.35 - 71.03: 110 71.03 - 94.71: 56 94.71 - 118.38: 42 Dihedral angle restraints: 12876 sinusoidal: 5805 harmonic: 7071 Sorted by residual: dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N TRP A 35 " pdb=" CA TRP A 35 " ideal model delta harmonic sigma weight residual 180.00 141.34 38.66 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA CYS A 196 " pdb=" C CYS A 196 " pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta harmonic sigma weight residual 180.00 142.55 37.45 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -148.17 62.17 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 12873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2910 0.095 - 0.190: 259 0.190 - 0.284: 23 0.284 - 0.379: 5 0.379 - 0.474: 1 Chirality restraints: 3198 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN I 197 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+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 2.47e+00 ... (remaining 3195 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 608 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO B 609 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 609 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 609 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 503 " 0.151 9.50e-02 1.11e+02 7.04e-02 7.19e+00 pdb=" NE ARG I 503 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG I 503 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG I 503 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG I 503 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 608 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO F 609 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 609 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 609 " 0.036 5.00e-02 4.00e+02 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 346 2.63 - 3.20: 19019 3.20 - 3.77: 28682 3.77 - 4.33: 37728 4.33 - 4.90: 60982 Nonbonded interactions: 146757 Sorted by model distance: nonbonded pdb=" OG SER I 447 " pdb=" O7 NAG T 1 " model vdw 2.064 3.040 nonbonded pdb=" OG SER E 447 " pdb=" O7 NAG Q 1 " model vdw 2.102 3.040 nonbonded pdb=" OG SER A 447 " pdb=" O7 NAG N 1 " model vdw 2.102 3.040 nonbonded pdb=" O VAL E 68 " pdb=" OG1 THR E 71 " model vdw 2.116 3.040 nonbonded pdb=" OE1 GLN B 591 " pdb=" OH TYR J 586 " model vdw 2.121 3.040 ... (remaining 146752 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = (chain 'N' and (resid 2 or resid 5 through 7)) selection = (chain 'O' and (resid 1 or resid 4 through 6)) selection = (chain 'Q' and (resid 2 or resid 5 through 7)) selection = (chain 'R' and (resid 1 or resid 4 through 6)) selection = (chain 'T' and (resid 2 or resid 5 through 7)) selection = (chain 'U' and (resid 1 or resid 4 through 6)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.790 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 0.102 20424 Z= 0.273 Angle : 1.087 19.039 27831 Z= 0.509 Chirality : 0.056 0.474 3198 Planarity : 0.006 0.092 3471 Dihedral : 16.779 118.383 8208 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.86 % Favored : 89.89 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.16), residues: 2424 helix: -0.28 (0.27), residues: 351 sheet: -1.40 (0.22), residues: 519 loop : -1.89 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG I 503 TYR 0.037 0.003 TYR B 643 PHE 0.034 0.003 PHE G 100D TRP 0.035 0.002 TRP I 45 HIS 0.008 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00588 (20334) covalent geometry : angle 0.96683 (27603) SS BOND : bond 0.00532 ( 42) SS BOND : angle 2.29503 ( 84) hydrogen bonds : bond 0.25003 ( 540) hydrogen bonds : angle 8.40807 ( 1458) link_ALPHA1-3 : bond 0.01761 ( 9) link_ALPHA1-3 : angle 8.16650 ( 27) link_ALPHA1-6 : bond 0.01130 ( 12) link_ALPHA1-6 : angle 3.42382 ( 36) link_BETA1-4 : bond 0.02254 ( 18) link_BETA1-4 : angle 8.73860 ( 54) link_NAG-ASN : bond 0.00968 ( 9) link_NAG-ASN : angle 3.32541 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 557 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.8432 (m-80) cc_final: 0.8078 (m-10) REVERT: A 102 ASP cc_start: 0.8874 (m-30) cc_final: 0.8504 (m-30) REVERT: A 177 TYR cc_start: 0.4691 (m-80) cc_final: 0.4357 (m-80) REVERT: A 180 ASP cc_start: 0.9002 (m-30) cc_final: 0.8768 (m-30) REVERT: A 192 ARG cc_start: 0.8005 (ptm160) cc_final: 0.7587 (ptt90) REVERT: A 216 HIS cc_start: 0.8241 (m-70) cc_final: 0.7821 (m-70) REVERT: A 217 TYR cc_start: 0.7266 (m-80) cc_final: 0.7014 (m-80) REVERT: A 351 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8740 (tptt) REVERT: A 369 MET cc_start: 0.7344 (mtt) cc_final: 0.7103 (mtt) REVERT: A 465 GLU cc_start: 0.8618 (pm20) cc_final: 0.8402 (mm-30) REVERT: B 571 TRP cc_start: 0.7082 (m-10) cc_final: 0.6711 (m-10) REVERT: B 591 GLN cc_start: 0.9392 (tp40) cc_final: 0.9153 (tp40) REVERT: C 39 LEU cc_start: 0.9225 (mm) cc_final: 0.8941 (mm) REVERT: C 52 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8361 (mtmt) REVERT: D 81 PHE cc_start: 0.6798 (p90) cc_final: 0.6403 (p90) REVERT: D 95 PHE cc_start: 0.7295 (m-10) cc_final: 0.7089 (m-10) REVERT: D 103 GLN cc_start: 0.7566 (pt0) cc_final: 0.6912 (pp30) REVERT: E 35 TRP cc_start: 0.5005 (m100) cc_final: 0.4765 (m100) REVERT: E 102 ASP cc_start: 0.9026 (m-30) cc_final: 0.8697 (m-30) REVERT: E 129 LEU cc_start: 0.7345 (mp) cc_final: 0.7086 (mp) REVERT: E 348 GLU cc_start: 0.7751 (tt0) cc_final: 0.7197 (tt0) REVERT: E 363 GLN cc_start: 0.8157 (pp30) cc_final: 0.7834 (pp30) REVERT: E 369 MET cc_start: 0.7360 (mtt) cc_final: 0.7017 (mtt) REVERT: E 383 PHE cc_start: 0.7506 (m-10) cc_final: 0.7250 (m-10) REVERT: E 426 MET cc_start: 0.8791 (ptp) cc_final: 0.7641 (tpt) REVERT: E 434 MET cc_start: 0.8455 (ptm) cc_final: 0.8225 (ppp) REVERT: E 460 THR cc_start: 0.8093 (p) cc_final: 0.7870 (p) REVERT: F 651 ASN cc_start: 0.8647 (m-40) cc_final: 0.8423 (m-40) REVERT: G 36 TRP cc_start: 0.8227 (m100) cc_final: 0.7643 (m100) REVERT: G 39 LEU cc_start: 0.9300 (mm) cc_final: 0.9033 (mm) REVERT: H 17 GLU cc_start: 0.8701 (mp0) cc_final: 0.8449 (mp0) REVERT: H 73 ILE cc_start: 0.9476 (mm) cc_final: 0.9101 (mm) REVERT: H 81 PHE cc_start: 0.7142 (p90) cc_final: 0.6681 (p90) REVERT: H 84 TYR cc_start: 0.7279 (p90) cc_final: 0.7069 (p90) REVERT: I 95 MET cc_start: 0.8699 (ppp) cc_final: 0.8451 (ppp) REVERT: I 159 PHE cc_start: 0.8507 (t80) cc_final: 0.8026 (t80) REVERT: I 180 ASP cc_start: 0.8953 (m-30) cc_final: 0.8453 (m-30) REVERT: I 252 ARG cc_start: 0.9027 (mpp80) cc_final: 0.8675 (mpt-90) REVERT: I 351 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8894 (tptt) REVERT: I 423 ILE cc_start: 0.9435 (mm) cc_final: 0.9107 (mm) REVERT: I 427 TRP cc_start: 0.7571 (m100) cc_final: 0.7060 (m100) REVERT: J 571 TRP cc_start: 0.6469 (m-10) cc_final: 0.6213 (m-10) REVERT: J 574 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8704 (mmtp) REVERT: J 607 ASN cc_start: 0.7902 (t0) cc_final: 0.7526 (t0) REVERT: J 651 ASN cc_start: 0.8810 (m-40) cc_final: 0.8503 (m-40) REVERT: K 28 GLU cc_start: 0.7865 (pm20) cc_final: 0.7597 (pm20) REVERT: K 31 ASP cc_start: 0.8759 (m-30) cc_final: 0.8556 (m-30) REVERT: K 36 TRP cc_start: 0.8267 (m100) cc_final: 0.7869 (m100) REVERT: K 89 VAL cc_start: 0.8706 (t) cc_final: 0.8399 (p) REVERT: K 96 LYS cc_start: 0.8227 (ptpt) cc_final: 0.8007 (ptpt) REVERT: L 80 ASP cc_start: 0.8388 (m-30) cc_final: 0.7897 (m-30) REVERT: L 81 PHE cc_start: 0.6766 (p90) cc_final: 0.5989 (p90) outliers start: 2 outliers final: 0 residues processed: 559 average time/residue: 0.1269 time to fit residues: 109.6064 Evaluate side-chains 433 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 94 ASN E 478 ASN F 577 GLN G 58 ASN G 100AASN H 103 GLN I 156 ASN ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN K 102 HIS L 103 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113388 restraints weight = 49952.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116613 restraints weight = 32407.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118897 restraints weight = 23671.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120529 restraints weight = 18794.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121685 restraints weight = 15851.231| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20424 Z= 0.222 Angle : 0.892 18.912 27831 Z= 0.426 Chirality : 0.053 0.405 3198 Planarity : 0.005 0.073 3471 Dihedral : 14.467 101.563 3603 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.48 % Favored : 89.27 % Rotamer: Outliers : 0.19 % Allowed : 4.59 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.16), residues: 2424 helix: 0.38 (0.30), residues: 315 sheet: -1.19 (0.24), residues: 468 loop : -1.86 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 503 TYR 0.032 0.003 TYR L 47 PHE 0.024 0.002 PHE L 60 TRP 0.023 0.002 TRP C 36 HIS 0.004 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00486 (20334) covalent geometry : angle 0.80313 (27603) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.48329 ( 84) hydrogen bonds : bond 0.05519 ( 540) hydrogen bonds : angle 6.26988 ( 1458) link_ALPHA1-3 : bond 0.01313 ( 9) link_ALPHA1-3 : angle 4.24545 ( 27) link_ALPHA1-6 : bond 0.00913 ( 12) link_ALPHA1-6 : angle 2.15782 ( 36) link_BETA1-4 : bond 0.02652 ( 18) link_BETA1-4 : angle 7.49115 ( 54) link_NAG-ASN : bond 0.00810 ( 9) link_NAG-ASN : angle 4.11483 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 530 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8907 (m-30) cc_final: 0.8577 (m-30) REVERT: A 177 TYR cc_start: 0.5414 (m-80) cc_final: 0.4533 (m-80) REVERT: A 180 ASP cc_start: 0.8855 (m-30) cc_final: 0.8553 (m-30) REVERT: A 370 GLU cc_start: 0.8159 (tp30) cc_final: 0.7808 (tp30) REVERT: B 574 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8396 (mttp) REVERT: B 575 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: B 648 GLU cc_start: 0.9227 (tt0) cc_final: 0.8696 (pt0) REVERT: C 37 ILE cc_start: 0.8779 (mt) cc_final: 0.8575 (tp) REVERT: C 39 LEU cc_start: 0.9393 (mm) cc_final: 0.9050 (mm) REVERT: D 81 PHE cc_start: 0.6938 (p90) cc_final: 0.6489 (p90) REVERT: D 103 GLN cc_start: 0.7682 (pt0) cc_final: 0.7268 (pp30) REVERT: E 102 ASP cc_start: 0.9018 (m-30) cc_final: 0.8714 (m-30) REVERT: E 426 MET cc_start: 0.8706 (ptp) cc_final: 0.8461 (tpt) REVERT: E 460 THR cc_start: 0.8365 (p) cc_final: 0.8159 (p) REVERT: F 651 ASN cc_start: 0.8770 (m-40) cc_final: 0.8558 (m-40) REVERT: G 36 TRP cc_start: 0.8384 (m100) cc_final: 0.7676 (m100) REVERT: G 46 GLU cc_start: 0.8095 (tp30) cc_final: 0.7886 (tp30) REVERT: G 89 VAL cc_start: 0.8737 (t) cc_final: 0.8378 (p) REVERT: H 13 LEU cc_start: 0.8552 (tp) cc_final: 0.8328 (mm) REVERT: H 72 THR cc_start: 0.8587 (t) cc_final: 0.8330 (t) REVERT: H 73 ILE cc_start: 0.9426 (mm) cc_final: 0.8956 (tp) REVERT: H 84 TYR cc_start: 0.7622 (p90) cc_final: 0.6900 (p90) REVERT: I 104 MET cc_start: 0.8939 (ttt) cc_final: 0.8510 (ttt) REVERT: I 159 PHE cc_start: 0.8498 (t80) cc_final: 0.8228 (t80) REVERT: I 180 ASP cc_start: 0.8939 (m-30) cc_final: 0.8576 (m-30) REVERT: I 351 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8858 (tptt) REVERT: I 370 GLU cc_start: 0.8247 (tp30) cc_final: 0.7852 (tp30) REVERT: I 426 MET cc_start: 0.8856 (ptp) cc_final: 0.8172 (tpt) REVERT: I 474 ASP cc_start: 0.8460 (t0) cc_final: 0.8239 (t0) REVERT: J 603 ILE cc_start: 0.8549 (mm) cc_final: 0.8311 (mm) REVERT: K 18 MET cc_start: 0.8539 (ppp) cc_final: 0.8303 (ppp) REVERT: K 28 GLU cc_start: 0.8142 (pm20) cc_final: 0.7834 (pm20) REVERT: K 31 ASP cc_start: 0.8850 (m-30) cc_final: 0.8591 (m-30) REVERT: K 36 TRP cc_start: 0.8643 (m100) cc_final: 0.8225 (m100) REVERT: K 82 LEU cc_start: 0.8844 (tp) cc_final: 0.8470 (tp) REVERT: K 96 LYS cc_start: 0.8482 (ptpt) cc_final: 0.8220 (ptpt) outliers start: 4 outliers final: 0 residues processed: 530 average time/residue: 0.1200 time to fit residues: 99.5305 Evaluate side-chains 414 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 17 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 234 optimal weight: 0.0470 chunk 71 optimal weight: 30.0000 chunk 224 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN B 577 GLN E 216 HIS E 300 ASN E 478 ASN G 58 ASN G 102 HIS H 103 GLN I 300 ASN J 575 GLN L 103 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116423 restraints weight = 49221.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119699 restraints weight = 31471.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121968 restraints weight = 22852.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123622 restraints weight = 18134.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124778 restraints weight = 15232.283| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20424 Z= 0.172 Angle : 0.838 18.066 27831 Z= 0.395 Chirality : 0.051 0.343 3198 Planarity : 0.005 0.065 3471 Dihedral : 13.267 96.569 3603 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.49 % Favored : 90.31 % Rotamer: Outliers : 0.28 % Allowed : 3.94 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.16), residues: 2424 helix: 0.37 (0.29), residues: 315 sheet: -1.12 (0.23), residues: 480 loop : -1.85 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 503 TYR 0.032 0.002 TYR H 47 PHE 0.024 0.002 PHE K 100D TRP 0.033 0.002 TRP H 33 HIS 0.005 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00370 (20334) covalent geometry : angle 0.75099 (27603) SS BOND : bond 0.00416 ( 42) SS BOND : angle 1.36839 ( 84) hydrogen bonds : bond 0.04626 ( 540) hydrogen bonds : angle 5.73940 ( 1458) link_ALPHA1-3 : bond 0.01377 ( 9) link_ALPHA1-3 : angle 4.30108 ( 27) link_ALPHA1-6 : bond 0.00849 ( 12) link_ALPHA1-6 : angle 1.96620 ( 36) link_BETA1-4 : bond 0.02699 ( 18) link_BETA1-4 : angle 7.15160 ( 54) link_NAG-ASN : bond 0.01043 ( 9) link_NAG-ASN : angle 3.91276 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 534 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.9001 (m-30) cc_final: 0.8661 (m-30) REVERT: A 177 TYR cc_start: 0.5469 (m-80) cc_final: 0.4688 (m-80) REVERT: A 369 MET cc_start: 0.7677 (mtt) cc_final: 0.7359 (mtt) REVERT: A 370 GLU cc_start: 0.8190 (tp30) cc_final: 0.7686 (tp30) REVERT: A 383 PHE cc_start: 0.7303 (m-10) cc_final: 0.7056 (m-10) REVERT: B 574 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8295 (mttp) REVERT: B 591 GLN cc_start: 0.9384 (tp40) cc_final: 0.9159 (tp-100) REVERT: C 37 ILE cc_start: 0.8862 (mt) cc_final: 0.8502 (tp) REVERT: C 39 LEU cc_start: 0.9457 (mm) cc_final: 0.9103 (mm) REVERT: C 48 MET cc_start: 0.8047 (tpp) cc_final: 0.7671 (tpp) REVERT: D 73 ILE cc_start: 0.9149 (tp) cc_final: 0.8948 (tp) REVERT: D 81 PHE cc_start: 0.6859 (p90) cc_final: 0.6428 (p90) REVERT: D 103 GLN cc_start: 0.7666 (pt0) cc_final: 0.7355 (pp30) REVERT: E 102 ASP cc_start: 0.9098 (m-30) cc_final: 0.8749 (m-30) REVERT: E 180 ASP cc_start: 0.8700 (m-30) cc_final: 0.8485 (m-30) REVERT: E 348 GLU cc_start: 0.7470 (tt0) cc_final: 0.7087 (tt0) REVERT: E 369 MET cc_start: 0.7497 (mtt) cc_final: 0.7211 (mtt) REVERT: E 383 PHE cc_start: 0.7347 (m-10) cc_final: 0.7106 (m-10) REVERT: E 460 THR cc_start: 0.7966 (p) cc_final: 0.7757 (p) REVERT: E 474 ASP cc_start: 0.8378 (t0) cc_final: 0.8114 (t0) REVERT: F 574 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8867 (mmtp) REVERT: G 36 TRP cc_start: 0.8311 (m100) cc_final: 0.7752 (m100) REVERT: G 46 GLU cc_start: 0.8022 (tp30) cc_final: 0.7753 (tp30) REVERT: G 100 ASN cc_start: 0.8966 (p0) cc_final: 0.8654 (p0) REVERT: H 13 LEU cc_start: 0.8481 (tp) cc_final: 0.8173 (mt) REVERT: H 73 ILE cc_start: 0.9375 (mm) cc_final: 0.8919 (tp) REVERT: H 84 TYR cc_start: 0.7364 (p90) cc_final: 0.6679 (p90) REVERT: I 104 MET cc_start: 0.8860 (ttt) cc_final: 0.8519 (ttt) REVERT: I 159 PHE cc_start: 0.8358 (t80) cc_final: 0.8045 (t80) REVERT: I 180 ASP cc_start: 0.8887 (m-30) cc_final: 0.8413 (m-30) REVERT: I 351 LYS cc_start: 0.9077 (tmtt) cc_final: 0.8821 (tptt) REVERT: I 423 ILE cc_start: 0.9568 (mm) cc_final: 0.9322 (mm) REVERT: I 474 ASP cc_start: 0.8110 (t0) cc_final: 0.7791 (t0) REVERT: J 574 LYS cc_start: 0.9266 (mmtm) cc_final: 0.9028 (mmtm) REVERT: J 651 ASN cc_start: 0.8753 (m-40) cc_final: 0.8446 (m-40) REVERT: K 28 GLU cc_start: 0.8153 (pm20) cc_final: 0.7898 (pm20) REVERT: K 36 TRP cc_start: 0.8587 (m100) cc_final: 0.8007 (m100) REVERT: K 39 LEU cc_start: 0.9245 (mm) cc_final: 0.8800 (mm) REVERT: K 82 LEU cc_start: 0.8792 (tp) cc_final: 0.8534 (tp) outliers start: 6 outliers final: 1 residues processed: 536 average time/residue: 0.1263 time to fit residues: 105.8954 Evaluate side-chains 417 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 416 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 228 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 58 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN F 575 GLN G 58 ASN H 103 GLN I 300 ASN I 478 ASN J 651 ASN L 103 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117516 restraints weight = 49079.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120762 restraints weight = 31774.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123079 restraints weight = 23161.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124754 restraints weight = 18330.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125913 restraints weight = 15399.884| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20424 Z= 0.150 Angle : 0.807 17.809 27831 Z= 0.377 Chirality : 0.051 0.358 3198 Planarity : 0.005 0.063 3471 Dihedral : 12.268 88.875 3603 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.45 % Favored : 90.35 % Rotamer: Outliers : 0.19 % Allowed : 3.56 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.16), residues: 2424 helix: 0.39 (0.30), residues: 315 sheet: -0.90 (0.23), residues: 477 loop : -1.83 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 44 TYR 0.027 0.002 TYR H 47 PHE 0.021 0.002 PHE C 100D TRP 0.035 0.002 TRP C 36 HIS 0.005 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00319 (20334) covalent geometry : angle 0.71955 (27603) SS BOND : bond 0.00395 ( 42) SS BOND : angle 1.30130 ( 84) hydrogen bonds : bond 0.04035 ( 540) hydrogen bonds : angle 5.46508 ( 1458) link_ALPHA1-3 : bond 0.01442 ( 9) link_ALPHA1-3 : angle 4.10300 ( 27) link_ALPHA1-6 : bond 0.00820 ( 12) link_ALPHA1-6 : angle 1.93837 ( 36) link_BETA1-4 : bond 0.02681 ( 18) link_BETA1-4 : angle 7.05977 ( 54) link_NAG-ASN : bond 0.00870 ( 9) link_NAG-ASN : angle 3.84229 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 527 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.5612 (m-80) cc_final: 0.4425 (m-80) REVERT: A 369 MET cc_start: 0.7676 (mtt) cc_final: 0.7368 (mtt) REVERT: A 370 GLU cc_start: 0.8201 (tp30) cc_final: 0.7785 (tp30) REVERT: B 571 TRP cc_start: 0.6929 (m-10) cc_final: 0.6285 (m-10) REVERT: B 591 GLN cc_start: 0.9382 (tp40) cc_final: 0.9026 (tp40) REVERT: C 37 ILE cc_start: 0.8728 (mt) cc_final: 0.8467 (tp) REVERT: C 51 LEU cc_start: 0.8612 (tt) cc_final: 0.8282 (mp) REVERT: C 69 MET cc_start: 0.8356 (ptm) cc_final: 0.8128 (ptm) REVERT: C 82 LEU cc_start: 0.8656 (pp) cc_final: 0.8114 (tp) REVERT: D 81 PHE cc_start: 0.6787 (p90) cc_final: 0.6347 (p90) REVERT: D 103 GLN cc_start: 0.7703 (pt0) cc_final: 0.7337 (pp30) REVERT: E 102 ASP cc_start: 0.9075 (m-30) cc_final: 0.8730 (m-30) REVERT: E 180 ASP cc_start: 0.8739 (m-30) cc_final: 0.8532 (m-30) REVERT: E 348 GLU cc_start: 0.7429 (tt0) cc_final: 0.7090 (tt0) REVERT: E 369 MET cc_start: 0.7492 (mtt) cc_final: 0.7196 (mtt) REVERT: E 474 ASP cc_start: 0.8196 (t0) cc_final: 0.7820 (t0) REVERT: F 574 LYS cc_start: 0.9162 (mmtp) cc_final: 0.8924 (mmtp) REVERT: F 623 TRP cc_start: 0.5737 (m100) cc_final: 0.5489 (m100) REVERT: F 626 MET cc_start: 0.6294 (tpp) cc_final: 0.5997 (tpt) REVERT: G 36 TRP cc_start: 0.8377 (m100) cc_final: 0.7940 (m100) REVERT: G 100 ASN cc_start: 0.8946 (p0) cc_final: 0.8665 (p0) REVERT: H 13 LEU cc_start: 0.8490 (tp) cc_final: 0.8218 (mt) REVERT: H 84 TYR cc_start: 0.7384 (p90) cc_final: 0.6804 (p90) REVERT: I 95 MET cc_start: 0.8936 (ppp) cc_final: 0.8411 (ppp) REVERT: I 104 MET cc_start: 0.8837 (ttt) cc_final: 0.8466 (ttt) REVERT: I 154 MET cc_start: 0.3016 (tpt) cc_final: 0.2258 (mmm) REVERT: I 180 ASP cc_start: 0.8812 (m-30) cc_final: 0.8287 (m-30) REVERT: I 308 ARG cc_start: 0.9072 (ttm-80) cc_final: 0.8743 (mmt90) REVERT: I 351 LYS cc_start: 0.9079 (tmtt) cc_final: 0.8840 (tptt) REVERT: I 369 MET cc_start: 0.7408 (mtt) cc_final: 0.7201 (mtt) REVERT: I 370 GLU cc_start: 0.8174 (tp30) cc_final: 0.7794 (tp30) REVERT: I 383 PHE cc_start: 0.7468 (m-10) cc_final: 0.7222 (m-10) REVERT: I 426 MET cc_start: 0.8747 (ptp) cc_final: 0.8091 (tpt) REVERT: I 494 LEU cc_start: 0.9337 (tp) cc_final: 0.8957 (tt) REVERT: J 574 LYS cc_start: 0.9253 (mmtp) cc_final: 0.8947 (mmtp) REVERT: J 603 ILE cc_start: 0.8673 (mm) cc_final: 0.8429 (mm) REVERT: J 651 ASN cc_start: 0.8787 (m110) cc_final: 0.8373 (m-40) REVERT: K 36 TRP cc_start: 0.8344 (m100) cc_final: 0.7820 (m100) REVERT: K 39 LEU cc_start: 0.9452 (mm) cc_final: 0.9084 (mm) REVERT: K 48 MET cc_start: 0.8564 (tpp) cc_final: 0.8231 (tpp) REVERT: K 82 LEU cc_start: 0.8824 (tp) cc_final: 0.8536 (tp) REVERT: K 96 LYS cc_start: 0.8926 (ptpp) cc_final: 0.8203 (ptpt) outliers start: 4 outliers final: 0 residues processed: 528 average time/residue: 0.1212 time to fit residues: 100.4037 Evaluate side-chains 413 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 116 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN E 478 ASN F 543 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN J 575 GLN J 651 ASN K 100AASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113546 restraints weight = 49535.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116685 restraints weight = 32354.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118933 restraints weight = 23778.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120443 restraints weight = 18960.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121468 restraints weight = 16147.718| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20424 Z= 0.205 Angle : 0.850 17.750 27831 Z= 0.403 Chirality : 0.053 0.377 3198 Planarity : 0.005 0.068 3471 Dihedral : 11.251 78.106 3603 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.34 % Favored : 88.49 % Rotamer: Outliers : 0.23 % Allowed : 3.23 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.16), residues: 2424 helix: 0.06 (0.29), residues: 333 sheet: -1.00 (0.23), residues: 483 loop : -1.91 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 503 TYR 0.031 0.002 TYR H 47 PHE 0.026 0.002 PHE K 100D TRP 0.026 0.002 TRP I 338 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00451 (20334) covalent geometry : angle 0.76629 (27603) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.41777 ( 84) hydrogen bonds : bond 0.04301 ( 540) hydrogen bonds : angle 5.53239 ( 1458) link_ALPHA1-3 : bond 0.01410 ( 9) link_ALPHA1-3 : angle 4.05469 ( 27) link_ALPHA1-6 : bond 0.00705 ( 12) link_ALPHA1-6 : angle 2.02539 ( 36) link_BETA1-4 : bond 0.02558 ( 18) link_BETA1-4 : angle 7.09919 ( 54) link_NAG-ASN : bond 0.00824 ( 9) link_NAG-ASN : angle 3.96035 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 524 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8580 (mmmm) REVERT: A 108 ILE cc_start: 0.9528 (mm) cc_final: 0.9211 (mm) REVERT: A 121 LYS cc_start: 0.9356 (mppt) cc_final: 0.9150 (mmtm) REVERT: A 370 GLU cc_start: 0.8231 (tp30) cc_final: 0.7849 (tp30) REVERT: A 434 MET cc_start: 0.8211 (ppp) cc_final: 0.7735 (ppp) REVERT: A 494 LEU cc_start: 0.9468 (tp) cc_final: 0.9100 (tt) REVERT: B 574 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8454 (mttp) REVERT: B 588 ARG cc_start: 0.8867 (ttt180) cc_final: 0.8553 (ttt180) REVERT: C 51 LEU cc_start: 0.8572 (tt) cc_final: 0.8313 (mp) REVERT: C 69 MET cc_start: 0.8403 (ptm) cc_final: 0.7835 (ptm) REVERT: C 80 LEU cc_start: 0.8900 (tt) cc_final: 0.8636 (tt) REVERT: C 81 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7827 (mt-10) REVERT: C 89 VAL cc_start: 0.8333 (t) cc_final: 0.8050 (p) REVERT: D 73 ILE cc_start: 0.9182 (tp) cc_final: 0.8773 (tp) REVERT: D 81 PHE cc_start: 0.6871 (p90) cc_final: 0.6443 (p90) REVERT: D 103 GLN cc_start: 0.7737 (pt0) cc_final: 0.7337 (pp30) REVERT: E 102 ASP cc_start: 0.9079 (m-30) cc_final: 0.8751 (m-30) REVERT: E 348 GLU cc_start: 0.7510 (tt0) cc_final: 0.7175 (tt0) REVERT: E 369 MET cc_start: 0.7514 (mtt) cc_final: 0.7178 (mtt) REVERT: E 383 PHE cc_start: 0.7497 (m-10) cc_final: 0.7247 (m-10) REVERT: E 426 MET cc_start: 0.8798 (ptp) cc_final: 0.8071 (tpt) REVERT: E 474 ASP cc_start: 0.8449 (t0) cc_final: 0.8158 (t0) REVERT: F 530 MET cc_start: 0.8332 (ptm) cc_final: 0.7299 (ptt) REVERT: F 574 LYS cc_start: 0.9215 (mmtp) cc_final: 0.8642 (mttp) REVERT: F 603 ILE cc_start: 0.8618 (mm) cc_final: 0.8319 (mm) REVERT: F 623 TRP cc_start: 0.6107 (m100) cc_final: 0.5544 (m100) REVERT: F 631 TRP cc_start: 0.7849 (t-100) cc_final: 0.7490 (t-100) REVERT: G 36 TRP cc_start: 0.8468 (m100) cc_final: 0.7682 (m100) REVERT: G 76 ASP cc_start: 0.6928 (t0) cc_final: 0.6475 (m-30) REVERT: G 100 TYR cc_start: 0.8196 (t80) cc_final: 0.7747 (t80) REVERT: G 100 ASN cc_start: 0.9123 (p0) cc_final: 0.8757 (p0) REVERT: H 84 TYR cc_start: 0.7666 (p90) cc_final: 0.7003 (p90) REVERT: I 121 LYS cc_start: 0.9354 (mppt) cc_final: 0.9140 (mptt) REVERT: I 154 MET cc_start: 0.3691 (tpt) cc_final: 0.3359 (tpt) REVERT: I 159 PHE cc_start: 0.8553 (t80) cc_final: 0.8257 (t80) REVERT: I 180 ASP cc_start: 0.8904 (m-30) cc_final: 0.8523 (m-30) REVERT: I 351 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8870 (tptt) REVERT: I 370 GLU cc_start: 0.8126 (tp30) cc_final: 0.7842 (tp30) REVERT: I 383 PHE cc_start: 0.7714 (m-10) cc_final: 0.7483 (m-10) REVERT: I 426 MET cc_start: 0.8857 (ptp) cc_final: 0.8013 (tpt) REVERT: I 474 ASP cc_start: 0.8407 (t0) cc_final: 0.8115 (t0) REVERT: I 494 LEU cc_start: 0.9420 (tp) cc_final: 0.8988 (tt) REVERT: J 530 MET cc_start: 0.7510 (mmp) cc_final: 0.7293 (mmp) REVERT: J 574 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8820 (mptt) REVERT: J 603 ILE cc_start: 0.8661 (mm) cc_final: 0.8431 (mm) REVERT: J 651 ASN cc_start: 0.8962 (m-40) cc_final: 0.8678 (m-40) REVERT: K 36 TRP cc_start: 0.8328 (m100) cc_final: 0.7698 (m100) REVERT: K 39 LEU cc_start: 0.9460 (mm) cc_final: 0.9198 (mm) REVERT: K 82 LEU cc_start: 0.8900 (tp) cc_final: 0.8658 (tp) REVERT: K 96 LYS cc_start: 0.8687 (ptpp) cc_final: 0.8335 (ptpt) REVERT: L 34 TYR cc_start: 0.8319 (m-10) cc_final: 0.7581 (m-10) outliers start: 5 outliers final: 0 residues processed: 528 average time/residue: 0.1412 time to fit residues: 118.0297 Evaluate side-chains 415 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 174 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 103 optimal weight: 0.0670 chunk 72 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 overall best weight: 2.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 478 ASN ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 300 ASN E 478 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN G 64 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN J 575 GLN K 100AASN K 102 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117638 restraints weight = 48413.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120923 restraints weight = 31232.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123280 restraints weight = 22749.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124945 restraints weight = 17979.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126107 restraints weight = 15079.115| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20424 Z= 0.144 Angle : 0.808 17.905 27831 Z= 0.377 Chirality : 0.052 0.383 3198 Planarity : 0.004 0.068 3471 Dihedral : 10.400 76.482 3603 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.16 % Favored : 90.68 % Rotamer: Outliers : 0.23 % Allowed : 1.45 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.16), residues: 2424 helix: 0.02 (0.28), residues: 333 sheet: -0.98 (0.22), residues: 522 loop : -1.84 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 503 TYR 0.032 0.002 TYR H 47 PHE 0.024 0.002 PHE K 100D TRP 0.036 0.002 TRP C 36 HIS 0.011 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00307 (20334) covalent geometry : angle 0.72331 (27603) SS BOND : bond 0.00313 ( 42) SS BOND : angle 1.19727 ( 84) hydrogen bonds : bond 0.03803 ( 540) hydrogen bonds : angle 5.33200 ( 1458) link_ALPHA1-3 : bond 0.01446 ( 9) link_ALPHA1-3 : angle 4.19368 ( 27) link_ALPHA1-6 : bond 0.00807 ( 12) link_ALPHA1-6 : angle 1.85932 ( 36) link_BETA1-4 : bond 0.02613 ( 18) link_BETA1-4 : angle 6.93732 ( 54) link_NAG-ASN : bond 0.01020 ( 9) link_NAG-ASN : angle 3.83876 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 536 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7692 (mtt) cc_final: 0.7354 (mtt) REVERT: A 370 GLU cc_start: 0.8127 (tp30) cc_final: 0.7786 (tp30) REVERT: A 383 PHE cc_start: 0.7196 (m-10) cc_final: 0.6996 (m-10) REVERT: A 494 LEU cc_start: 0.9424 (tp) cc_final: 0.9075 (tt) REVERT: B 574 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8307 (mttp) REVERT: B 588 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8478 (ttt180) REVERT: C 13 LYS cc_start: 0.9342 (mmtp) cc_final: 0.9081 (mmtp) REVERT: D 81 PHE cc_start: 0.6743 (p90) cc_final: 0.6130 (p90) REVERT: D 103 GLN cc_start: 0.7588 (pt0) cc_final: 0.7266 (pp30) REVERT: E 102 ASP cc_start: 0.9048 (m-30) cc_final: 0.8663 (m-30) REVERT: E 348 GLU cc_start: 0.7261 (tt0) cc_final: 0.7017 (tt0) REVERT: E 369 MET cc_start: 0.7479 (mtt) cc_final: 0.7156 (mtt) REVERT: E 383 PHE cc_start: 0.7377 (m-10) cc_final: 0.7171 (m-10) REVERT: E 474 ASP cc_start: 0.8440 (t0) cc_final: 0.7957 (t0) REVERT: E 479 TRP cc_start: 0.8962 (m100) cc_final: 0.8441 (m-10) REVERT: F 530 MET cc_start: 0.8217 (ptm) cc_final: 0.7669 (ptt) REVERT: F 535 MET cc_start: 0.8606 (ttm) cc_final: 0.8222 (mmm) REVERT: F 574 LYS cc_start: 0.9180 (mmtp) cc_final: 0.8704 (mttp) REVERT: F 603 ILE cc_start: 0.8433 (mm) cc_final: 0.8180 (mm) REVERT: F 623 TRP cc_start: 0.6021 (m100) cc_final: 0.5558 (m100) REVERT: F 631 TRP cc_start: 0.7764 (t-100) cc_final: 0.7490 (t-100) REVERT: F 651 ASN cc_start: 0.8578 (m-40) cc_final: 0.8357 (m-40) REVERT: G 36 TRP cc_start: 0.8399 (m100) cc_final: 0.7798 (m100) REVERT: G 76 ASP cc_start: 0.6906 (t0) cc_final: 0.6504 (m-30) REVERT: G 100 TYR cc_start: 0.8224 (t80) cc_final: 0.7773 (t80) REVERT: G 100 ASN cc_start: 0.9175 (p0) cc_final: 0.8829 (p0) REVERT: H 13 LEU cc_start: 0.8479 (mt) cc_final: 0.8265 (mt) REVERT: H 81 PHE cc_start: 0.6897 (p90) cc_final: 0.6465 (p90) REVERT: H 84 TYR cc_start: 0.7493 (p90) cc_final: 0.6962 (p90) REVERT: I 95 MET cc_start: 0.8812 (ppp) cc_final: 0.8176 (ppp) REVERT: I 104 MET cc_start: 0.9018 (ttt) cc_final: 0.7995 (ttt) REVERT: I 108 ILE cc_start: 0.9534 (mm) cc_final: 0.9258 (mm) REVERT: I 159 PHE cc_start: 0.8529 (t80) cc_final: 0.8109 (t80) REVERT: I 180 ASP cc_start: 0.8817 (m-30) cc_final: 0.8316 (m-30) REVERT: I 203 GLN cc_start: 0.8562 (tp40) cc_final: 0.8327 (tp40) REVERT: I 351 LYS cc_start: 0.9105 (tmtt) cc_final: 0.8881 (tptt) REVERT: I 370 GLU cc_start: 0.8106 (tp30) cc_final: 0.7657 (tp30) REVERT: I 383 PHE cc_start: 0.7567 (m-10) cc_final: 0.7307 (m-10) REVERT: I 423 ILE cc_start: 0.9542 (mm) cc_final: 0.9274 (mm) REVERT: I 474 ASP cc_start: 0.8370 (t0) cc_final: 0.7964 (t0) REVERT: I 479 TRP cc_start: 0.9003 (m-10) cc_final: 0.8405 (m-10) REVERT: I 494 LEU cc_start: 0.9438 (tp) cc_final: 0.9157 (tt) REVERT: J 530 MET cc_start: 0.7531 (mmp) cc_final: 0.7301 (mmp) REVERT: J 574 LYS cc_start: 0.9168 (mmtp) cc_final: 0.8857 (mptt) REVERT: J 586 TYR cc_start: 0.9080 (t80) cc_final: 0.8810 (t80) REVERT: J 643 TYR cc_start: 0.8365 (m-80) cc_final: 0.8138 (m-80) REVERT: J 651 ASN cc_start: 0.8905 (m-40) cc_final: 0.8584 (m-40) REVERT: K 36 TRP cc_start: 0.8261 (m100) cc_final: 0.7713 (m100) REVERT: K 39 LEU cc_start: 0.9461 (mm) cc_final: 0.9109 (mm) REVERT: K 82 LEU cc_start: 0.8775 (tp) cc_final: 0.8471 (tp) REVERT: K 96 LYS cc_start: 0.8697 (ptpp) cc_final: 0.7502 (ptpt) REVERT: K 101 GLU cc_start: 0.8374 (mp0) cc_final: 0.7978 (mp0) REVERT: L 34 TYR cc_start: 0.8199 (m-10) cc_final: 0.7743 (m-10) outliers start: 5 outliers final: 0 residues processed: 539 average time/residue: 0.1436 time to fit residues: 121.4414 Evaluate side-chains 431 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN B 543 ASN C 58 ASN E 229 ASN E 478 ASN F 543 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN G 64 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN J 630 GLN K 100AASN L 103 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112670 restraints weight = 50107.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.115732 restraints weight = 32791.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117854 restraints weight = 24186.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119350 restraints weight = 19435.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120422 restraints weight = 16547.714| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20424 Z= 0.232 Angle : 0.878 17.533 27831 Z= 0.421 Chirality : 0.054 0.393 3198 Planarity : 0.005 0.090 3471 Dihedral : 9.887 73.803 3603 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.21 % Favored : 87.62 % Rotamer: Outliers : 0.33 % Allowed : 2.30 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.16), residues: 2424 helix: -0.08 (0.28), residues: 333 sheet: -1.17 (0.24), residues: 468 loop : -1.87 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 432 TYR 0.038 0.003 TYR H 47 PHE 0.020 0.003 PHE K 100D TRP 0.024 0.002 TRP I 338 HIS 0.009 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00516 (20334) covalent geometry : angle 0.80096 (27603) SS BOND : bond 0.00674 ( 42) SS BOND : angle 1.42672 ( 84) hydrogen bonds : bond 0.04338 ( 540) hydrogen bonds : angle 5.60990 ( 1458) link_ALPHA1-3 : bond 0.01367 ( 9) link_ALPHA1-3 : angle 4.04733 ( 27) link_ALPHA1-6 : bond 0.00640 ( 12) link_ALPHA1-6 : angle 2.03053 ( 36) link_BETA1-4 : bond 0.02519 ( 18) link_BETA1-4 : angle 6.87433 ( 54) link_NAG-ASN : bond 0.00812 ( 9) link_NAG-ASN : angle 3.94126 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 505 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8515 (tpp) cc_final: 0.8305 (tpp) REVERT: A 121 LYS cc_start: 0.9391 (mppt) cc_final: 0.9112 (mmtt) REVERT: A 369 MET cc_start: 0.7850 (mtt) cc_final: 0.7633 (mtm) REVERT: A 370 GLU cc_start: 0.8146 (tp30) cc_final: 0.7724 (tp30) REVERT: A 383 PHE cc_start: 0.7361 (m-10) cc_final: 0.7064 (m-10) REVERT: A 434 MET cc_start: 0.8303 (ppp) cc_final: 0.8019 (ppp) REVERT: A 485 LYS cc_start: 0.8677 (mttt) cc_final: 0.8284 (mttt) REVERT: A 494 LEU cc_start: 0.9472 (tp) cc_final: 0.9141 (tt) REVERT: B 574 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8227 (mttp) REVERT: B 624 ASP cc_start: 0.7667 (m-30) cc_final: 0.7465 (m-30) REVERT: C 89 VAL cc_start: 0.8511 (t) cc_final: 0.8088 (p) REVERT: D 13 LEU cc_start: 0.8706 (pt) cc_final: 0.8232 (pp) REVERT: D 81 PHE cc_start: 0.6891 (p90) cc_final: 0.6182 (p90) REVERT: E 369 MET cc_start: 0.7599 (mtt) cc_final: 0.7204 (mtt) REVERT: E 383 PHE cc_start: 0.7403 (m-10) cc_final: 0.7111 (m-10) REVERT: E 426 MET cc_start: 0.8803 (ptp) cc_final: 0.7566 (tpt) REVERT: E 474 ASP cc_start: 0.8556 (t0) cc_final: 0.8344 (t0) REVERT: F 535 MET cc_start: 0.8658 (ttm) cc_final: 0.8344 (mmm) REVERT: F 574 LYS cc_start: 0.9226 (mmtp) cc_final: 0.8870 (mptt) REVERT: F 603 ILE cc_start: 0.8502 (mm) cc_final: 0.8191 (mm) REVERT: F 648 GLU cc_start: 0.9302 (pt0) cc_final: 0.9045 (pt0) REVERT: G 100 TYR cc_start: 0.8499 (t80) cc_final: 0.8071 (t80) REVERT: G 100 ASN cc_start: 0.9201 (p0) cc_final: 0.8813 (p0) REVERT: H 81 PHE cc_start: 0.7062 (p90) cc_final: 0.6506 (p90) REVERT: H 84 TYR cc_start: 0.7762 (p90) cc_final: 0.7148 (p90) REVERT: I 104 MET cc_start: 0.9081 (ttt) cc_final: 0.8030 (ttt) REVERT: I 108 ILE cc_start: 0.9532 (mm) cc_final: 0.9293 (mm) REVERT: I 121 LYS cc_start: 0.9386 (mppt) cc_final: 0.9133 (mptt) REVERT: I 159 PHE cc_start: 0.8354 (t80) cc_final: 0.8112 (t80) REVERT: I 180 ASP cc_start: 0.8899 (m-30) cc_final: 0.8587 (m-30) REVERT: I 282 LYS cc_start: 0.9409 (mttm) cc_final: 0.8945 (mtmt) REVERT: I 308 ARG cc_start: 0.9082 (ttm-80) cc_final: 0.8831 (mmt90) REVERT: I 351 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8843 (tptt) REVERT: I 369 MET cc_start: 0.7572 (mtt) cc_final: 0.7339 (mtt) REVERT: I 370 GLU cc_start: 0.8069 (tp30) cc_final: 0.7711 (tp30) REVERT: I 383 PHE cc_start: 0.7750 (m-10) cc_final: 0.7492 (m-10) REVERT: I 474 ASP cc_start: 0.8604 (t0) cc_final: 0.8383 (t0) REVERT: I 479 TRP cc_start: 0.9145 (m-10) cc_final: 0.8462 (m-10) REVERT: I 494 LEU cc_start: 0.9447 (tp) cc_final: 0.9182 (tt) REVERT: J 574 LYS cc_start: 0.9194 (mmtp) cc_final: 0.8863 (mptt) REVERT: J 603 ILE cc_start: 0.8646 (mm) cc_final: 0.8387 (mm) REVERT: J 643 TYR cc_start: 0.8396 (m-80) cc_final: 0.8129 (m-80) REVERT: J 651 ASN cc_start: 0.8988 (m-40) cc_final: 0.8706 (m-40) REVERT: K 18 MET cc_start: 0.8495 (ppp) cc_final: 0.8240 (ppp) REVERT: K 39 LEU cc_start: 0.9500 (mm) cc_final: 0.9068 (mm) REVERT: K 82 LEU cc_start: 0.8836 (tp) cc_final: 0.8534 (tp) REVERT: K 96 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8079 (ptpt) REVERT: K 101 GLU cc_start: 0.8451 (mp0) cc_final: 0.8171 (mp0) REVERT: L 34 TYR cc_start: 0.8406 (m-10) cc_final: 0.8015 (m-10) outliers start: 7 outliers final: 0 residues processed: 510 average time/residue: 0.1426 time to fit residues: 114.5338 Evaluate side-chains 409 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 101 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 543 ASN G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN J 575 GLN K 100AASN L 103 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115910 restraints weight = 48762.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119265 restraints weight = 30945.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121570 restraints weight = 22371.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123011 restraints weight = 17703.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124296 restraints weight = 15021.421| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20424 Z= 0.161 Angle : 0.832 17.529 27831 Z= 0.393 Chirality : 0.052 0.388 3198 Planarity : 0.005 0.071 3471 Dihedral : 9.504 72.515 3603 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.49 % Favored : 90.35 % Rotamer: Outliers : 0.23 % Allowed : 1.27 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.16), residues: 2424 helix: 0.25 (0.29), residues: 312 sheet: -1.10 (0.24), residues: 480 loop : -1.82 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 503 TYR 0.035 0.002 TYR H 47 PHE 0.023 0.002 PHE K 100D TRP 0.029 0.002 TRP I 338 HIS 0.004 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00353 (20334) covalent geometry : angle 0.75236 (27603) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.35481 ( 84) hydrogen bonds : bond 0.03996 ( 540) hydrogen bonds : angle 5.34875 ( 1458) link_ALPHA1-3 : bond 0.01428 ( 9) link_ALPHA1-3 : angle 4.17936 ( 27) link_ALPHA1-6 : bond 0.00673 ( 12) link_ALPHA1-6 : angle 1.81050 ( 36) link_BETA1-4 : bond 0.02558 ( 18) link_BETA1-4 : angle 6.79025 ( 54) link_NAG-ASN : bond 0.00718 ( 9) link_NAG-ASN : angle 3.86490 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 519 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.8222 (m-10) cc_final: 0.8014 (m-10) REVERT: A 95 MET cc_start: 0.8789 (ppp) cc_final: 0.8051 (ppp) REVERT: A 108 ILE cc_start: 0.9448 (mm) cc_final: 0.9121 (mm) REVERT: A 369 MET cc_start: 0.7698 (mtt) cc_final: 0.7377 (mtt) REVERT: A 370 GLU cc_start: 0.8076 (tp30) cc_final: 0.7769 (tp30) REVERT: A 383 PHE cc_start: 0.7214 (m-10) cc_final: 0.6967 (m-10) REVERT: A 434 MET cc_start: 0.8264 (ppp) cc_final: 0.7815 (ppp) REVERT: B 574 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8225 (mttp) REVERT: C 46 GLU cc_start: 0.8210 (pp20) cc_final: 0.7882 (pp20) REVERT: D 13 LEU cc_start: 0.8588 (pt) cc_final: 0.7888 (mt) REVERT: E 96 TRP cc_start: 0.5842 (p90) cc_final: 0.5574 (p90) REVERT: E 154 MET cc_start: 0.3349 (tpt) cc_final: 0.2709 (tpt) REVERT: E 203 GLN cc_start: 0.8893 (tp40) cc_final: 0.8655 (tp40) REVERT: E 369 MET cc_start: 0.7467 (mtt) cc_final: 0.7098 (mtt) REVERT: E 383 PHE cc_start: 0.7459 (m-10) cc_final: 0.7162 (m-10) REVERT: E 426 MET cc_start: 0.8655 (ptp) cc_final: 0.7573 (tpt) REVERT: E 474 ASP cc_start: 0.8572 (t0) cc_final: 0.8184 (t0) REVERT: E 479 TRP cc_start: 0.9051 (m100) cc_final: 0.8563 (m-10) REVERT: F 530 MET cc_start: 0.8107 (ptm) cc_final: 0.7551 (ptm) REVERT: F 535 MET cc_start: 0.8675 (ttm) cc_final: 0.8321 (mmm) REVERT: F 574 LYS cc_start: 0.9203 (mmtp) cc_final: 0.8826 (mttt) REVERT: F 623 TRP cc_start: 0.6349 (m100) cc_final: 0.5958 (m100) REVERT: F 631 TRP cc_start: 0.7819 (t-100) cc_final: 0.7456 (t-100) REVERT: F 651 ASN cc_start: 0.8628 (m-40) cc_final: 0.8408 (m-40) REVERT: G 76 ASP cc_start: 0.6853 (t0) cc_final: 0.6535 (m-30) REVERT: G 100 TYR cc_start: 0.8497 (t80) cc_final: 0.7929 (t80) REVERT: G 100 ASN cc_start: 0.9226 (p0) cc_final: 0.8864 (p0) REVERT: H 81 PHE cc_start: 0.7097 (p90) cc_final: 0.6561 (p90) REVERT: H 84 TYR cc_start: 0.7719 (p90) cc_final: 0.7277 (p90) REVERT: I 95 MET cc_start: 0.8754 (ppp) cc_final: 0.8184 (ppp) REVERT: I 97 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8664 (mptt) REVERT: I 104 MET cc_start: 0.9071 (ttt) cc_final: 0.8099 (ttt) REVERT: I 108 ILE cc_start: 0.9522 (mm) cc_final: 0.9282 (mm) REVERT: I 180 ASP cc_start: 0.8839 (m-30) cc_final: 0.8434 (m-30) REVERT: I 203 GLN cc_start: 0.8601 (tp40) cc_final: 0.8328 (tp40) REVERT: I 308 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8600 (mmt90) REVERT: I 351 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8761 (tptt) REVERT: I 370 GLU cc_start: 0.8050 (tp30) cc_final: 0.7723 (tp30) REVERT: I 383 PHE cc_start: 0.7640 (m-10) cc_final: 0.7358 (m-10) REVERT: I 479 TRP cc_start: 0.9041 (m-10) cc_final: 0.8471 (m-10) REVERT: I 494 LEU cc_start: 0.9411 (tp) cc_final: 0.9156 (tt) REVERT: J 574 LYS cc_start: 0.9209 (mmtp) cc_final: 0.8909 (mptt) REVERT: J 585 ARG cc_start: 0.9147 (tpp80) cc_final: 0.8838 (tpp80) REVERT: J 589 ASP cc_start: 0.8336 (m-30) cc_final: 0.7965 (m-30) REVERT: J 603 ILE cc_start: 0.8445 (mm) cc_final: 0.8216 (mm) REVERT: J 643 TYR cc_start: 0.8455 (m-80) cc_final: 0.8173 (m-80) REVERT: J 651 ASN cc_start: 0.8908 (m-40) cc_final: 0.8614 (m-40) REVERT: K 18 MET cc_start: 0.8414 (ppp) cc_final: 0.8162 (ppp) REVERT: K 39 LEU cc_start: 0.9537 (mm) cc_final: 0.9125 (mm) REVERT: K 43 LYS cc_start: 0.9170 (mmtp) cc_final: 0.8968 (mmmm) REVERT: K 82 LEU cc_start: 0.8714 (tp) cc_final: 0.8445 (tp) REVERT: K 96 LYS cc_start: 0.8850 (ptpp) cc_final: 0.8089 (ptpt) REVERT: K 101 GLU cc_start: 0.8291 (mp0) cc_final: 0.7870 (mp0) REVERT: L 34 TYR cc_start: 0.8273 (m-10) cc_final: 0.8024 (m-10) outliers start: 5 outliers final: 0 residues processed: 521 average time/residue: 0.1420 time to fit residues: 116.0567 Evaluate side-chains 422 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 190 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 53 optimal weight: 0.1980 chunk 184 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 179 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 64 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 478 ASN F 543 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN J 575 GLN K 100AASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117626 restraints weight = 48345.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120890 restraints weight = 31117.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123182 restraints weight = 22638.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124805 restraints weight = 17930.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125979 restraints weight = 15074.399| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20424 Z= 0.155 Angle : 0.829 17.508 27831 Z= 0.391 Chirality : 0.052 0.401 3198 Planarity : 0.005 0.068 3471 Dihedral : 9.228 71.481 3603 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.11 % Favored : 89.73 % Rotamer: Outliers : 0.19 % Allowed : 0.52 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.16), residues: 2424 helix: 0.21 (0.30), residues: 312 sheet: -1.01 (0.24), residues: 492 loop : -1.80 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 37 TYR 0.042 0.002 TYR J 586 PHE 0.025 0.002 PHE K 100D TRP 0.059 0.003 TRP H 33 HIS 0.006 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00339 (20334) covalent geometry : angle 0.74978 (27603) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.30635 ( 84) hydrogen bonds : bond 0.03923 ( 540) hydrogen bonds : angle 5.34234 ( 1458) link_ALPHA1-3 : bond 0.01391 ( 9) link_ALPHA1-3 : angle 4.18630 ( 27) link_ALPHA1-6 : bond 0.00654 ( 12) link_ALPHA1-6 : angle 1.79489 ( 36) link_BETA1-4 : bond 0.02597 ( 18) link_BETA1-4 : angle 6.75549 ( 54) link_NAG-ASN : bond 0.00757 ( 9) link_NAG-ASN : angle 3.80483 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 512 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.8352 (m-10) cc_final: 0.8060 (m-10) REVERT: A 180 ASP cc_start: 0.8521 (m-30) cc_final: 0.8206 (m-30) REVERT: A 369 MET cc_start: 0.7700 (mtt) cc_final: 0.7494 (mtm) REVERT: A 370 GLU cc_start: 0.8141 (tp30) cc_final: 0.7831 (tp30) REVERT: A 383 PHE cc_start: 0.7209 (m-10) cc_final: 0.6973 (m-10) REVERT: A 423 ILE cc_start: 0.9531 (mm) cc_final: 0.9140 (mm) REVERT: A 434 MET cc_start: 0.8224 (ppp) cc_final: 0.7722 (ppp) REVERT: B 574 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8260 (mttp) REVERT: B 634 GLU cc_start: 0.8474 (mp0) cc_final: 0.8209 (mp0) REVERT: C 46 GLU cc_start: 0.8218 (pp20) cc_final: 0.7984 (pp20) REVERT: D 13 LEU cc_start: 0.8564 (pt) cc_final: 0.7828 (mt) REVERT: D 60 PHE cc_start: 0.8607 (m-80) cc_final: 0.8325 (m-80) REVERT: D 73 ILE cc_start: 0.9135 (tp) cc_final: 0.8740 (tp) REVERT: E 49 LYS cc_start: 0.8937 (tmtt) cc_final: 0.8610 (tmtt) REVERT: E 93 PHE cc_start: 0.8340 (m-10) cc_final: 0.8063 (m-80) REVERT: E 154 MET cc_start: 0.3135 (tpt) cc_final: 0.2512 (tpt) REVERT: E 369 MET cc_start: 0.7479 (mtt) cc_final: 0.7096 (mtt) REVERT: E 426 MET cc_start: 0.8606 (ptp) cc_final: 0.7212 (tpt) REVERT: E 460 THR cc_start: 0.7521 (p) cc_final: 0.7292 (p) REVERT: E 474 ASP cc_start: 0.8451 (t0) cc_final: 0.8194 (t0) REVERT: E 479 TRP cc_start: 0.9003 (m100) cc_final: 0.8569 (m-10) REVERT: F 530 MET cc_start: 0.8023 (ptm) cc_final: 0.7245 (ptt) REVERT: F 535 MET cc_start: 0.8649 (ttm) cc_final: 0.8297 (mmm) REVERT: F 574 LYS cc_start: 0.9175 (mmtp) cc_final: 0.8833 (mttt) REVERT: F 623 TRP cc_start: 0.6381 (m100) cc_final: 0.5760 (m100) REVERT: F 651 ASN cc_start: 0.8685 (m-40) cc_final: 0.8444 (m-40) REVERT: G 76 ASP cc_start: 0.6793 (t0) cc_final: 0.6501 (m-30) REVERT: G 100 ASN cc_start: 0.9192 (p0) cc_final: 0.7692 (p0) REVERT: G 100 TRP cc_start: 0.7737 (m100) cc_final: 0.7005 (m100) REVERT: G 100 ASP cc_start: 0.8204 (p0) cc_final: 0.7834 (p0) REVERT: H 60 PHE cc_start: 0.8817 (m-80) cc_final: 0.8502 (m-80) REVERT: H 81 PHE cc_start: 0.7015 (p90) cc_final: 0.6446 (p90) REVERT: I 97 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8636 (mptt) REVERT: I 104 MET cc_start: 0.9105 (ttt) cc_final: 0.8112 (ttt) REVERT: I 108 ILE cc_start: 0.9533 (mm) cc_final: 0.9276 (mm) REVERT: I 159 PHE cc_start: 0.8464 (t80) cc_final: 0.8139 (t80) REVERT: I 180 ASP cc_start: 0.8756 (m-30) cc_final: 0.8286 (m-30) REVERT: I 308 ARG cc_start: 0.8992 (ttm-80) cc_final: 0.8613 (mmt90) REVERT: I 351 LYS cc_start: 0.9010 (tmtt) cc_final: 0.8737 (tptt) REVERT: I 370 GLU cc_start: 0.8019 (tp30) cc_final: 0.7815 (tp30) REVERT: I 383 PHE cc_start: 0.7564 (m-10) cc_final: 0.7202 (m-10) REVERT: I 423 ILE cc_start: 0.9592 (mm) cc_final: 0.9352 (mm) REVERT: I 426 MET cc_start: 0.8287 (ptp) cc_final: 0.7438 (tpt) REVERT: I 474 ASP cc_start: 0.8297 (t0) cc_final: 0.8072 (t0) REVERT: I 479 TRP cc_start: 0.9041 (m-10) cc_final: 0.8431 (m-10) REVERT: J 574 LYS cc_start: 0.9195 (mmtp) cc_final: 0.8912 (mptt) REVERT: J 585 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8816 (tpp80) REVERT: J 589 ASP cc_start: 0.8394 (m-30) cc_final: 0.7944 (m-30) REVERT: J 643 TYR cc_start: 0.8384 (m-80) cc_final: 0.8068 (m-80) REVERT: J 651 ASN cc_start: 0.8899 (m-40) cc_final: 0.8600 (m-40) REVERT: K 18 MET cc_start: 0.8423 (ppp) cc_final: 0.8221 (ppp) REVERT: K 39 LEU cc_start: 0.9523 (mm) cc_final: 0.9127 (mm) REVERT: K 82 LEU cc_start: 0.8714 (tp) cc_final: 0.8421 (tp) REVERT: K 96 LYS cc_start: 0.8748 (ptpp) cc_final: 0.7840 (ptpt) REVERT: K 101 GLU cc_start: 0.8122 (mp0) cc_final: 0.7871 (mp0) outliers start: 4 outliers final: 2 residues processed: 515 average time/residue: 0.1203 time to fit residues: 96.3976 Evaluate side-chains 422 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 45 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 148 optimal weight: 0.0970 chunk 169 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 64 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 543 ASN F 575 GLN G 58 ASN G 64 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN J 575 GLN K 100AASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114642 restraints weight = 48326.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117864 restraints weight = 31227.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120158 restraints weight = 22843.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121765 restraints weight = 18133.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122800 restraints weight = 15322.378| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20424 Z= 0.181 Angle : 0.843 17.439 27831 Z= 0.402 Chirality : 0.053 0.400 3198 Planarity : 0.005 0.070 3471 Dihedral : 9.139 69.962 3603 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.14 % Favored : 88.66 % Rotamer: Outliers : 0.14 % Allowed : 0.75 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.16), residues: 2424 helix: 0.25 (0.30), residues: 312 sheet: -1.00 (0.24), residues: 486 loop : -1.81 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 71 TYR 0.037 0.002 TYR H 47 PHE 0.027 0.002 PHE F 522 TRP 0.042 0.002 TRP H 33 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00400 (20334) covalent geometry : angle 0.76637 (27603) SS BOND : bond 0.00477 ( 42) SS BOND : angle 1.30021 ( 84) hydrogen bonds : bond 0.04074 ( 540) hydrogen bonds : angle 5.42020 ( 1458) link_ALPHA1-3 : bond 0.01362 ( 9) link_ALPHA1-3 : angle 4.15297 ( 27) link_ALPHA1-6 : bond 0.00581 ( 12) link_ALPHA1-6 : angle 1.83829 ( 36) link_BETA1-4 : bond 0.02535 ( 18) link_BETA1-4 : angle 6.73233 ( 54) link_NAG-ASN : bond 0.00688 ( 9) link_NAG-ASN : angle 3.80261 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 497 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.8379 (m-10) cc_final: 0.8094 (m-10) REVERT: A 95 MET cc_start: 0.8677 (ppp) cc_final: 0.8380 (ppp) REVERT: A 121 LYS cc_start: 0.9366 (mppt) cc_final: 0.9145 (mmtm) REVERT: A 270 ILE cc_start: 0.8230 (mm) cc_final: 0.8024 (mm) REVERT: A 369 MET cc_start: 0.7698 (mtt) cc_final: 0.7445 (ttm) REVERT: A 370 GLU cc_start: 0.8167 (tp30) cc_final: 0.7854 (tp30) REVERT: A 383 PHE cc_start: 0.7247 (m-10) cc_final: 0.6977 (m-10) REVERT: A 434 MET cc_start: 0.8246 (ppp) cc_final: 0.7737 (ppp) REVERT: B 574 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8261 (mttp) REVERT: B 634 GLU cc_start: 0.8517 (mp0) cc_final: 0.8160 (mp0) REVERT: C 46 GLU cc_start: 0.8290 (pp20) cc_final: 0.7948 (pp20) REVERT: C 48 MET cc_start: 0.8052 (tpp) cc_final: 0.7839 (tpp) REVERT: D 13 LEU cc_start: 0.8577 (pt) cc_final: 0.7855 (mt) REVERT: D 60 PHE cc_start: 0.8731 (m-80) cc_final: 0.8511 (m-80) REVERT: E 93 PHE cc_start: 0.8277 (m-10) cc_final: 0.8030 (m-80) REVERT: E 154 MET cc_start: 0.3410 (tpt) cc_final: 0.2722 (tpt) REVERT: E 369 MET cc_start: 0.7464 (mtt) cc_final: 0.7126 (mtt) REVERT: E 426 MET cc_start: 0.8067 (ptp) cc_final: 0.7053 (tpt) REVERT: E 474 ASP cc_start: 0.8608 (t0) cc_final: 0.8210 (t0) REVERT: E 479 TRP cc_start: 0.9034 (m100) cc_final: 0.8608 (m-10) REVERT: E 485 LYS cc_start: 0.8808 (mttt) cc_final: 0.8437 (mttt) REVERT: F 535 MET cc_start: 0.8668 (ttm) cc_final: 0.8282 (mmm) REVERT: F 574 LYS cc_start: 0.9229 (mmtp) cc_final: 0.8755 (mttp) REVERT: F 648 GLU cc_start: 0.9309 (pt0) cc_final: 0.9036 (pt0) REVERT: F 651 ASN cc_start: 0.8708 (m-40) cc_final: 0.8494 (m-40) REVERT: G 76 ASP cc_start: 0.6896 (t0) cc_final: 0.6545 (m-30) REVERT: G 100 ASN cc_start: 0.9245 (p0) cc_final: 0.7823 (p0) REVERT: G 100 TRP cc_start: 0.7742 (m100) cc_final: 0.7104 (m100) REVERT: G 100 ASP cc_start: 0.8180 (p0) cc_final: 0.7913 (p0) REVERT: H 60 PHE cc_start: 0.8892 (m-80) cc_final: 0.8603 (m-80) REVERT: H 81 PHE cc_start: 0.7101 (p90) cc_final: 0.6495 (p90) REVERT: H 84 TYR cc_start: 0.7804 (p90) cc_final: 0.7460 (p90) REVERT: H 95 PHE cc_start: 0.8495 (m-10) cc_final: 0.8287 (m-10) REVERT: I 97 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8604 (mptt) REVERT: I 104 MET cc_start: 0.9109 (ttt) cc_final: 0.8110 (ttt) REVERT: I 108 ILE cc_start: 0.9542 (mm) cc_final: 0.9296 (mm) REVERT: I 154 MET cc_start: 0.3167 (tpt) cc_final: 0.2840 (tpt) REVERT: I 180 ASP cc_start: 0.8803 (m-30) cc_final: 0.8398 (m-30) REVERT: I 270 ILE cc_start: 0.8299 (mm) cc_final: 0.8047 (mm) REVERT: I 308 ARG cc_start: 0.9055 (ttm-80) cc_final: 0.8689 (mmt90) REVERT: I 351 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8734 (tptt) REVERT: I 369 MET cc_start: 0.7561 (mtt) cc_final: 0.7310 (mtt) REVERT: I 370 GLU cc_start: 0.8014 (tp30) cc_final: 0.7749 (tp30) REVERT: I 479 TRP cc_start: 0.9099 (m-10) cc_final: 0.8507 (m-10) REVERT: J 585 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8713 (tpp80) REVERT: J 589 ASP cc_start: 0.8446 (m-30) cc_final: 0.7978 (m-30) REVERT: J 651 ASN cc_start: 0.8912 (m-40) cc_final: 0.8629 (m-40) REVERT: K 82 LEU cc_start: 0.8741 (tp) cc_final: 0.8500 (tp) REVERT: K 96 LYS cc_start: 0.8672 (ptpt) cc_final: 0.8097 (ptpt) REVERT: K 101 GLU cc_start: 0.8200 (mp0) cc_final: 0.7970 (mp0) REVERT: L 60 PHE cc_start: 0.8481 (m-80) cc_final: 0.8279 (m-80) outliers start: 3 outliers final: 0 residues processed: 499 average time/residue: 0.1310 time to fit residues: 103.0251 Evaluate side-chains 410 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 11 optimal weight: 10.0000 chunk 177 optimal weight: 0.0670 chunk 207 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 14 optimal weight: 0.0870 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN E 478 ASN G 58 ASN G 64 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN K 100AASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.143531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120614 restraints weight = 48020.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124018 restraints weight = 30606.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126404 restraints weight = 22086.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128122 restraints weight = 17370.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129340 restraints weight = 14500.629| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20424 Z= 0.140 Angle : 0.816 17.580 27831 Z= 0.383 Chirality : 0.052 0.435 3198 Planarity : 0.004 0.066 3471 Dihedral : 8.833 68.944 3603 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.33 % Favored : 91.50 % Rotamer: Outliers : 0.14 % Allowed : 0.23 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.16), residues: 2424 helix: 0.41 (0.30), residues: 312 sheet: -0.79 (0.25), residues: 456 loop : -1.72 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 24 TYR 0.033 0.002 TYR H 47 PHE 0.028 0.002 PHE K 100D TRP 0.037 0.002 TRP H 33 HIS 0.005 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00292 (20334) covalent geometry : angle 0.73821 (27603) SS BOND : bond 0.00395 ( 42) SS BOND : angle 1.11113 ( 84) hydrogen bonds : bond 0.03774 ( 540) hydrogen bonds : angle 5.13738 ( 1458) link_ALPHA1-3 : bond 0.01427 ( 9) link_ALPHA1-3 : angle 4.30870 ( 27) link_ALPHA1-6 : bond 0.00705 ( 12) link_ALPHA1-6 : angle 1.67083 ( 36) link_BETA1-4 : bond 0.02614 ( 18) link_BETA1-4 : angle 6.69011 ( 54) link_NAG-ASN : bond 0.00754 ( 9) link_NAG-ASN : angle 3.71420 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.69 seconds wall clock time: 53 minutes 24.91 seconds (3204.91 seconds total)