Starting phenix.real_space_refine on Tue Jun 17 11:58:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8san_40274/06_2025/8san_40274_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8san_40274/06_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_40274/06_2025/8san_40274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8san_40274/06_2025/8san_40274.map" model { file = "/net/cci-nas-00/data/ceres_data/8san_40274/06_2025/8san_40274_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8san_40274/06_2025/8san_40274_neut.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.04, per 1000 atoms: 0.60 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: 5.36 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.74 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: 7.25 Time building geometry restraints manager: 6.35 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: 0.570 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: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.650 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.380 ------------------------------------------------------------------------------- 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 : 5.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.002 TRP I 45 HIS 0.008 0.001 HIS E 249 PHE 0.034 0.003 PHE G 100D TYR 0.037 0.003 TYR B 643 ARG 0.036 0.001 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00968 ( 9) link_NAG-ASN : angle 3.32541 ( 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_ALPHA1-3 : bond 0.01761 ( 9) link_ALPHA1-3 : angle 8.16650 ( 27) hydrogen bonds : bond 0.25003 ( 540) hydrogen bonds : angle 8.40807 ( 1458) SS BOND : bond 0.00532 ( 42) SS BOND : angle 2.29503 ( 84) covalent geometry : bond 0.00588 (20334) covalent geometry : angle 0.96683 (27603) *********************** 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 : 2.274 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: 0.8077 (m-10) REVERT: A 102 ASP cc_start: 0.8874 (m-30) cc_final: 0.8506 (m-30) REVERT: A 177 TYR cc_start: 0.4691 (m-80) cc_final: 0.4354 (m-80) REVERT: A 180 ASP cc_start: 0.9002 (m-30) cc_final: 0.8767 (m-30) REVERT: A 192 ARG cc_start: 0.8005 (ptm160) cc_final: 0.7589 (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: 0.7013 (m-80) REVERT: A 351 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8744 (tptt) REVERT: A 369 MET cc_start: 0.7344 (mtt) cc_final: 0.7102 (mtt) REVERT: A 465 GLU cc_start: 0.8618 (pm20) cc_final: 0.8405 (mm-30) REVERT: B 571 TRP cc_start: 0.7082 (m-10) cc_final: 0.6710 (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: 0.8944 (mm) REVERT: C 52 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8359 (mtmt) REVERT: D 81 PHE cc_start: 0.6798 (p90) cc_final: 0.6310 (p90) REVERT: D 95 PHE cc_start: 0.7295 (m-10) cc_final: 0.7093 (m-10) REVERT: D 103 GLN cc_start: 0.7566 (pt0) cc_final: 0.6936 (pp30) REVERT: E 35 TRP cc_start: 0.5005 (m100) cc_final: 0.4762 (m100) REVERT: E 102 ASP cc_start: 0.9026 (m-30) cc_final: 0.8699 (m-30) REVERT: E 348 GLU cc_start: 0.7751 (tt0) cc_final: 0.7193 (tt0) REVERT: E 363 GLN cc_start: 0.8157 (pp30) cc_final: 0.7836 (pp30) REVERT: E 369 MET cc_start: 0.7360 (mtt) cc_final: 0.7020 (mtt) REVERT: E 383 PHE cc_start: 0.7506 (m-10) cc_final: 0.7254 (m-10) REVERT: E 426 MET cc_start: 0.8791 (ptp) cc_final: 0.7640 (tpt) REVERT: E 434 MET cc_start: 0.8455 (ptm) cc_final: 0.8224 (ppp) REVERT: E 460 THR cc_start: 0.8093 (p) cc_final: 0.7865 (p) REVERT: F 651 ASN cc_start: 0.8647 (m-40) cc_final: 0.8427 (m-40) REVERT: G 36 TRP cc_start: 0.8227 (m100) cc_final: 0.7667 (m100) REVERT: G 39 LEU cc_start: 0.9300 (mm) cc_final: 0.9033 (mm) REVERT: H 73 ILE cc_start: 0.9476 (mm) cc_final: 0.9100 (mm) REVERT: H 81 PHE cc_start: 0.7142 (p90) cc_final: 0.6682 (p90) REVERT: H 84 TYR cc_start: 0.7279 (p90) cc_final: 0.7068 (p90) REVERT: I 95 MET cc_start: 0.8699 (ppp) cc_final: 0.8454 (ppp) REVERT: I 159 PHE cc_start: 0.8507 (t80) cc_final: 0.8025 (t80) REVERT: I 180 ASP cc_start: 0.8953 (m-30) cc_final: 0.8448 (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: 0.8892 (tptt) REVERT: I 423 ILE cc_start: 0.9435 (mm) cc_final: 0.9110 (mm) REVERT: J 571 TRP cc_start: 0.6469 (m-10) cc_final: 0.6223 (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: 0.7530 (t0) REVERT: J 651 ASN cc_start: 0.8810 (m-40) cc_final: 0.8502 (m-40) REVERT: K 28 GLU cc_start: 0.7865 (pm20) cc_final: 0.7596 (pm20) REVERT: K 36 TRP cc_start: 0.8267 (m100) cc_final: 0.7867 (m100) REVERT: K 89 VAL cc_start: 0.8706 (t) cc_final: 0.8396 (p) REVERT: K 96 LYS cc_start: 0.8227 (ptpt) cc_final: 0.8010 (ptpt) REVERT: L 80 ASP cc_start: 0.8388 (m-30) cc_final: 0.7902 (m-30) REVERT: L 81 PHE cc_start: 0.6766 (p90) cc_final: 0.5987 (p90) outliers start: 2 outliers final: 0 residues processed: 559 average time/residue: 0.3070 time to fit residues: 261.6155 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 : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 300 ASN E 478 ASN F 577 GLN G 58 ASN G 100AASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN L 103 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116159 restraints weight = 49626.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119430 restraints weight = 31884.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121750 restraints weight = 23164.239| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20424 Z= 0.191 Angle : 0.866 19.285 27831 Z= 0.411 Chirality : 0.053 0.401 3198 Planarity : 0.005 0.071 3471 Dihedral : 14.493 102.183 3603 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.61 % Favored : 90.14 % Rotamer: Outliers : 0.19 % Allowed : 4.22 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.16), residues: 2424 helix: 0.45 (0.30), residues: 315 sheet: -1.15 (0.24), residues: 468 loop : -1.82 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 36 HIS 0.004 0.001 HIS G 102 PHE 0.023 0.002 PHE L 60 TYR 0.033 0.002 TYR L 47 ARG 0.008 0.001 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.01012 ( 9) link_NAG-ASN : angle 3.98207 ( 27) link_ALPHA1-6 : bond 0.00983 ( 12) link_ALPHA1-6 : angle 2.13192 ( 36) link_BETA1-4 : bond 0.02555 ( 18) link_BETA1-4 : angle 7.51938 ( 54) link_ALPHA1-3 : bond 0.01306 ( 9) link_ALPHA1-3 : angle 4.24792 ( 27) hydrogen bonds : bond 0.05204 ( 540) hydrogen bonds : angle 6.20217 ( 1458) SS BOND : bond 0.00489 ( 42) SS BOND : angle 1.44025 ( 84) covalent geometry : bond 0.00412 (20334) covalent geometry : angle 0.77475 (27603) *********************** 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 541 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 537 time to evaluate : 2.135 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 91 GLU cc_start: 0.8213 (tp30) cc_final: 0.8002 (tm-30) REVERT: A 102 ASP cc_start: 0.8896 (m-30) cc_final: 0.8556 (m-30) REVERT: A 177 TYR cc_start: 0.5395 (m-80) cc_final: 0.4646 (m-80) REVERT: A 180 ASP cc_start: 0.8832 (m-30) cc_final: 0.8532 (m-30) REVERT: A 216 HIS cc_start: 0.8381 (m-70) cc_final: 0.8121 (m90) REVERT: A 370 GLU cc_start: 0.8198 (tp30) cc_final: 0.7827 (tp30) REVERT: B 574 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8309 (mttp) REVERT: C 39 LEU cc_start: 0.9445 (mm) cc_final: 0.9197 (mm) REVERT: C 51 LEU cc_start: 0.8386 (tt) cc_final: 0.8003 (mp) REVERT: C 69 MET cc_start: 0.8654 (ptm) cc_final: 0.8071 (ptm) REVERT: D 34 TYR cc_start: 0.8125 (m-10) cc_final: 0.7883 (m-10) REVERT: D 81 PHE cc_start: 0.6918 (p90) cc_final: 0.6365 (p90) REVERT: D 103 GLN cc_start: 0.7769 (pt0) cc_final: 0.7344 (pp30) REVERT: E 102 ASP cc_start: 0.9036 (m-30) cc_final: 0.8719 (m-30) REVERT: E 104 MET cc_start: 0.8614 (tpp) cc_final: 0.8356 (mmt) REVERT: E 217 TYR cc_start: 0.6685 (m-10) cc_final: 0.4477 (m-10) REVERT: E 426 MET cc_start: 0.8710 (ptp) cc_final: 0.8422 (tpt) REVERT: E 460 THR cc_start: 0.8247 (p) cc_final: 0.8025 (p) REVERT: F 651 ASN cc_start: 0.8798 (m-40) cc_final: 0.8571 (m-40) REVERT: G 36 TRP cc_start: 0.8350 (m100) cc_final: 0.7789 (m100) REVERT: G 89 VAL cc_start: 0.8751 (t) cc_final: 0.8378 (p) REVERT: G 96 LYS cc_start: 0.8523 (ptpt) cc_final: 0.8259 (ptpt) REVERT: G 100 TYR cc_start: 0.8327 (t80) cc_final: 0.8005 (t80) REVERT: H 84 TYR cc_start: 0.7462 (p90) cc_final: 0.6889 (p90) REVERT: I 159 PHE cc_start: 0.8522 (t80) cc_final: 0.8164 (t80) REVERT: I 180 ASP cc_start: 0.8869 (m-30) cc_final: 0.8345 (m-30) REVERT: I 351 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8898 (tptt) REVERT: I 370 GLU cc_start: 0.8240 (tp30) cc_final: 0.7848 (tp30) REVERT: I 426 MET cc_start: 0.8849 (ptp) cc_final: 0.8275 (tpt) REVERT: I 474 ASP cc_start: 0.8488 (t0) cc_final: 0.8283 (t0) REVERT: J 603 ILE cc_start: 0.8486 (mm) cc_final: 0.8270 (mm) REVERT: K 18 MET cc_start: 0.8517 (ppp) cc_final: 0.8265 (ppp) REVERT: K 36 TRP cc_start: 0.8581 (m100) cc_final: 0.8182 (m100) REVERT: K 48 MET cc_start: 0.8803 (tpp) cc_final: 0.8313 (tpp) REVERT: K 82 LEU cc_start: 0.8763 (tp) cc_final: 0.8470 (tp) REVERT: K 96 LYS cc_start: 0.8432 (ptpt) cc_final: 0.8177 (ptpt) outliers start: 4 outliers final: 1 residues processed: 537 average time/residue: 0.3040 time to fit residues: 252.8015 Evaluate side-chains 410 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 146 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN E 478 ASN G 58 ASN G 102 HIS H 103 GLN I 156 ASN ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN K 102 HIS L 103 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116524 restraints weight = 49146.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119755 restraints weight = 31927.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122031 restraints weight = 23304.315| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2090 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= 0.179 Angle : 0.837 17.916 27831 Z= 0.395 Chirality : 0.051 0.341 3198 Planarity : 0.005 0.063 3471 Dihedral : 13.288 96.492 3603 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.31 % Favored : 89.48 % Rotamer: Outliers : 0.19 % Allowed : 3.75 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2424 helix: 0.42 (0.30), residues: 315 sheet: -1.07 (0.23), residues: 480 loop : -1.81 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 33 HIS 0.005 0.001 HIS K 102 PHE 0.024 0.002 PHE A 53 TYR 0.020 0.002 TYR B 586 ARG 0.008 0.001 ARG I 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 9) link_NAG-ASN : angle 3.93642 ( 27) link_ALPHA1-6 : bond 0.00818 ( 12) link_ALPHA1-6 : angle 1.98616 ( 36) link_BETA1-4 : bond 0.02709 ( 18) link_BETA1-4 : angle 7.18692 ( 54) link_ALPHA1-3 : bond 0.01345 ( 9) link_ALPHA1-3 : angle 4.27458 ( 27) hydrogen bonds : bond 0.04592 ( 540) hydrogen bonds : angle 5.72779 ( 1458) SS BOND : bond 0.00631 ( 42) SS BOND : angle 1.33108 ( 84) covalent geometry : bond 0.00388 (20334) covalent geometry : angle 0.74906 (27603) *********************** 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 531 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 527 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.9012 (m-30) cc_final: 0.8632 (m-30) REVERT: A 154 MET cc_start: 0.2082 (tpt) cc_final: 0.1094 (mmm) REVERT: A 177 TYR cc_start: 0.5838 (m-80) cc_final: 0.4629 (m-80) REVERT: A 180 ASP cc_start: 0.8846 (m-30) cc_final: 0.8562 (m-30) REVERT: A 351 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8771 (tptt) REVERT: A 369 MET cc_start: 0.7677 (mtt) cc_final: 0.7395 (mtt) REVERT: A 370 GLU cc_start: 0.8260 (tp30) cc_final: 0.7731 (tp30) REVERT: A 383 PHE cc_start: 0.7272 (m-10) cc_final: 0.7041 (m-10) REVERT: B 574 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8354 (mttp) REVERT: B 591 GLN cc_start: 0.9388 (tp40) cc_final: 0.9160 (tp-100) REVERT: C 28 GLU cc_start: 0.8363 (pm20) cc_final: 0.8096 (pm20) REVERT: C 31 ASP cc_start: 0.8645 (m-30) cc_final: 0.8280 (m-30) REVERT: C 39 LEU cc_start: 0.9512 (mm) cc_final: 0.9227 (mm) REVERT: C 48 MET cc_start: 0.7758 (tpp) cc_final: 0.7525 (tpp) REVERT: C 51 LEU cc_start: 0.8549 (tt) cc_final: 0.8222 (mp) REVERT: D 81 PHE cc_start: 0.6820 (p90) cc_final: 0.6393 (p90) REVERT: D 103 GLN cc_start: 0.7729 (pt0) cc_final: 0.7321 (pp30) REVERT: E 104 MET cc_start: 0.8275 (tpp) cc_final: 0.8042 (mmt) REVERT: E 180 ASP cc_start: 0.8700 (m-30) cc_final: 0.8489 (m-30) REVERT: E 279 ASN cc_start: 0.7996 (t0) cc_final: 0.7733 (p0) REVERT: E 369 MET cc_start: 0.7513 (mtt) cc_final: 0.7227 (mtt) REVERT: E 383 PHE cc_start: 0.7377 (m-10) cc_final: 0.7113 (m-10) REVERT: E 426 MET cc_start: 0.8727 (ptp) cc_final: 0.8298 (tpt) REVERT: E 474 ASP cc_start: 0.8511 (t0) cc_final: 0.8251 (t0) REVERT: F 522 PHE cc_start: 0.6908 (m-10) cc_final: 0.6698 (m-10) REVERT: F 631 TRP cc_start: 0.7728 (t-100) cc_final: 0.7353 (t-100) REVERT: G 36 TRP cc_start: 0.8291 (m100) cc_final: 0.7775 (m100) REVERT: G 100 TYR cc_start: 0.8332 (t80) cc_final: 0.7950 (t80) REVERT: G 100 ASN cc_start: 0.8965 (p0) cc_final: 0.8703 (p0) REVERT: H 84 TYR cc_start: 0.7315 (p90) cc_final: 0.6758 (p90) REVERT: I 104 MET cc_start: 0.8931 (ttt) cc_final: 0.8665 (ttt) REVERT: I 159 PHE cc_start: 0.8345 (t80) cc_final: 0.8034 (t80) REVERT: I 180 ASP cc_start: 0.8872 (m-30) cc_final: 0.8407 (m-30) REVERT: I 351 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8858 (tptt) REVERT: I 423 ILE cc_start: 0.9577 (mm) cc_final: 0.9334 (mm) REVERT: J 651 ASN cc_start: 0.8759 (m-40) cc_final: 0.8498 (m-40) REVERT: K 18 MET cc_start: 0.8617 (ppp) cc_final: 0.8390 (ppp) REVERT: K 36 TRP cc_start: 0.8554 (m100) cc_final: 0.8118 (m100) REVERT: K 39 LEU cc_start: 0.9281 (mm) cc_final: 0.8854 (mm) REVERT: K 48 MET cc_start: 0.8744 (tpp) cc_final: 0.8322 (tpp) REVERT: K 82 LEU cc_start: 0.8765 (tp) cc_final: 0.8500 (tp) outliers start: 4 outliers final: 0 residues processed: 528 average time/residue: 0.2979 time to fit residues: 243.6426 Evaluate side-chains 419 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 47 optimal weight: 30.0000 chunk 75 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 172 optimal weight: 0.0980 chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN E 216 HIS ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN J 575 GLN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113891 restraints weight = 49349.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117037 restraints weight = 32067.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119280 restraints weight = 23522.312| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20424 Z= 0.189 Angle : 0.829 17.562 27831 Z= 0.392 Chirality : 0.051 0.366 3198 Planarity : 0.005 0.066 3471 Dihedral : 12.200 87.181 3603 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.85 % Favored : 88.94 % Rotamer: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.16), residues: 2424 helix: 0.40 (0.30), residues: 315 sheet: -0.99 (0.23), residues: 486 loop : -1.85 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 36 HIS 0.006 0.001 HIS K 102 PHE 0.016 0.002 PHE A 53 TYR 0.017 0.002 TYR H 47 ARG 0.006 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00864 ( 9) link_NAG-ASN : angle 3.87901 ( 27) link_ALPHA1-6 : bond 0.00744 ( 12) link_ALPHA1-6 : angle 2.00782 ( 36) link_BETA1-4 : bond 0.02622 ( 18) link_BETA1-4 : angle 7.03643 ( 54) link_ALPHA1-3 : bond 0.01353 ( 9) link_ALPHA1-3 : angle 4.06603 ( 27) hydrogen bonds : bond 0.04275 ( 540) hydrogen bonds : angle 5.57853 ( 1458) SS BOND : bond 0.00593 ( 42) SS BOND : angle 1.23902 ( 84) covalent geometry : bond 0.00413 (20334) covalent geometry : angle 0.74568 (27603) *********************** 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 520 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 517 time to evaluate : 2.094 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 351 LYS cc_start: 0.8999 (tmtt) cc_final: 0.8790 (tptt) REVERT: A 369 MET cc_start: 0.7729 (mtt) cc_final: 0.7285 (mtt) REVERT: A 370 GLU cc_start: 0.8275 (tp30) cc_final: 0.7868 (tp30) REVERT: A 383 PHE cc_start: 0.7286 (m-10) cc_final: 0.7061 (m-10) REVERT: A 434 MET cc_start: 0.8246 (ppp) cc_final: 0.7754 (ppp) REVERT: B 574 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8541 (mttp) REVERT: B 591 GLN cc_start: 0.9403 (tp40) cc_final: 0.9027 (tp40) REVERT: C 39 LEU cc_start: 0.9533 (mm) cc_final: 0.9244 (mm) REVERT: C 46 GLU cc_start: 0.8252 (pp20) cc_final: 0.8016 (pp20) REVERT: C 51 LEU cc_start: 0.8690 (tt) cc_final: 0.8212 (mp) REVERT: D 81 PHE cc_start: 0.6932 (p90) cc_final: 0.6274 (p90) REVERT: D 103 GLN cc_start: 0.7775 (pt0) cc_final: 0.7406 (pp30) REVERT: E 279 ASN cc_start: 0.8049 (t0) cc_final: 0.7799 (p0) REVERT: E 348 GLU cc_start: 0.7562 (tt0) cc_final: 0.7212 (tt0) REVERT: E 369 MET cc_start: 0.7614 (mtt) cc_final: 0.7291 (mtt) REVERT: E 426 MET cc_start: 0.8727 (ptp) cc_final: 0.8195 (tpt) REVERT: E 474 ASP cc_start: 0.8286 (t0) cc_final: 0.8037 (t0) REVERT: F 574 LYS cc_start: 0.9115 (mmtp) cc_final: 0.8728 (mptt) REVERT: G 36 TRP cc_start: 0.8480 (m100) cc_final: 0.7872 (m100) REVERT: G 100 TYR cc_start: 0.8286 (t80) cc_final: 0.8003 (t80) REVERT: G 100 ASN cc_start: 0.8990 (p0) cc_final: 0.8656 (p0) REVERT: H 56 ILE cc_start: 0.8037 (mm) cc_final: 0.7830 (mm) REVERT: H 84 TYR cc_start: 0.7448 (p90) cc_final: 0.6916 (p90) REVERT: I 108 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9050 (mp) REVERT: I 121 LYS cc_start: 0.9289 (mppt) cc_final: 0.9075 (mmtm) REVERT: I 180 ASP cc_start: 0.8926 (m-30) cc_final: 0.8617 (m-30) REVERT: I 351 LYS cc_start: 0.9124 (tmtt) cc_final: 0.8855 (tptt) REVERT: I 370 GLU cc_start: 0.8250 (tp30) cc_final: 0.7901 (tp30) REVERT: I 383 PHE cc_start: 0.7613 (m-10) cc_final: 0.7368 (m-10) REVERT: I 426 MET cc_start: 0.9009 (ptp) cc_final: 0.8049 (tpt) REVERT: I 479 TRP cc_start: 0.9102 (m-10) cc_final: 0.8661 (m-10) REVERT: I 494 LEU cc_start: 0.9346 (tp) cc_final: 0.9015 (tt) REVERT: J 530 MET cc_start: 0.8053 (mmm) cc_final: 0.7843 (mmp) REVERT: J 574 LYS cc_start: 0.9367 (mmtm) cc_final: 0.9147 (mmtm) REVERT: J 603 ILE cc_start: 0.8710 (mm) cc_final: 0.8421 (mm) REVERT: J 651 ASN cc_start: 0.8920 (m-40) cc_final: 0.8630 (m-40) REVERT: K 18 MET cc_start: 0.8556 (ppp) cc_final: 0.8354 (ppp) REVERT: K 36 TRP cc_start: 0.8533 (m100) cc_final: 0.8061 (m100) REVERT: K 39 LEU cc_start: 0.9509 (mm) cc_final: 0.9111 (mm) REVERT: K 48 MET cc_start: 0.8708 (tpp) cc_final: 0.8353 (tpp) REVERT: K 82 LEU cc_start: 0.8873 (tp) cc_final: 0.8669 (tp) REVERT: K 96 LYS cc_start: 0.8387 (ptpt) cc_final: 0.7787 (ptpt) REVERT: L 47 TYR cc_start: 0.7725 (m-80) cc_final: 0.7353 (m-80) outliers start: 3 outliers final: 0 residues processed: 519 average time/residue: 0.2970 time to fit residues: 238.8762 Evaluate side-chains 412 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 228 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 237 optimal weight: 0.0060 chunk 11 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN E 300 ASN E 478 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118419 restraints weight = 48725.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121817 restraints weight = 31200.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124220 restraints weight = 22471.260| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2654 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= 0.138 Angle : 0.804 18.221 27831 Z= 0.371 Chirality : 0.051 0.359 3198 Planarity : 0.004 0.065 3471 Dihedral : 11.346 80.120 3603 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.79 % Favored : 91.05 % Rotamer: Outliers : 0.09 % Allowed : 2.25 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2424 helix: 0.53 (0.30), residues: 315 sheet: -0.79 (0.23), residues: 483 loop : -1.81 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 623 HIS 0.004 0.001 HIS G 102 PHE 0.023 0.002 PHE C 100D TYR 0.018 0.002 TYR H 47 ARG 0.006 0.000 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00985 ( 9) link_NAG-ASN : angle 4.00160 ( 27) link_ALPHA1-6 : bond 0.00834 ( 12) link_ALPHA1-6 : angle 1.90975 ( 36) link_BETA1-4 : bond 0.02577 ( 18) link_BETA1-4 : angle 7.15933 ( 54) link_ALPHA1-3 : bond 0.01432 ( 9) link_ALPHA1-3 : angle 4.15815 ( 27) hydrogen bonds : bond 0.03874 ( 540) hydrogen bonds : angle 5.28483 ( 1458) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.21160 ( 84) covalent geometry : bond 0.00289 (20334) covalent geometry : angle 0.71372 (27603) *********************** 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 545 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 543 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.2469 (tpt) cc_final: 0.1656 (mmm) REVERT: A 351 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8735 (tptt) REVERT: A 369 MET cc_start: 0.7683 (mtt) cc_final: 0.7360 (mtt) REVERT: A 370 GLU cc_start: 0.8231 (tp30) cc_final: 0.7835 (tp30) REVERT: A 383 PHE cc_start: 0.7155 (m-10) cc_final: 0.6927 (m-10) REVERT: A 434 MET cc_start: 0.8159 (ppp) cc_final: 0.7726 (ppp) REVERT: B 571 TRP cc_start: 0.6911 (m-10) cc_final: 0.6043 (m-10) REVERT: B 591 GLN cc_start: 0.9417 (tp40) cc_final: 0.9070 (tp40) REVERT: C 28 GLU cc_start: 0.8333 (pm20) cc_final: 0.8123 (pm20) REVERT: C 80 LEU cc_start: 0.8802 (tt) cc_final: 0.8431 (tt) REVERT: D 81 PHE cc_start: 0.6748 (p90) cc_final: 0.6137 (p90) REVERT: D 103 GLN cc_start: 0.7751 (pt0) cc_final: 0.7420 (pp30) REVERT: E 102 ASP cc_start: 0.9022 (m-30) cc_final: 0.8757 (m-30) REVERT: E 279 ASN cc_start: 0.8043 (t0) cc_final: 0.7753 (p0) REVERT: E 348 GLU cc_start: 0.7390 (tt0) cc_final: 0.7169 (tt0) REVERT: E 369 MET cc_start: 0.7504 (mtt) cc_final: 0.7217 (mtt) REVERT: E 474 ASP cc_start: 0.8392 (t0) cc_final: 0.7951 (t0) REVERT: F 574 LYS cc_start: 0.9134 (mmtp) cc_final: 0.8812 (mttp) REVERT: F 575 GLN cc_start: 0.8946 (mt0) cc_final: 0.8639 (mp10) REVERT: F 603 ILE cc_start: 0.8612 (mm) cc_final: 0.8327 (mm) REVERT: F 631 TRP cc_start: 0.7774 (t-100) cc_final: 0.7352 (t-100) REVERT: G 36 TRP cc_start: 0.8328 (m100) cc_final: 0.7746 (m100) REVERT: G 76 ASP cc_start: 0.6973 (t0) cc_final: 0.6433 (m-30) REVERT: G 96 LYS cc_start: 0.8404 (ptpt) cc_final: 0.7997 (ptpt) REVERT: G 100 ASN cc_start: 0.9029 (p0) cc_final: 0.8669 (p0) REVERT: G 100 ASP cc_start: 0.8148 (p0) cc_final: 0.7890 (p0) REVERT: H 81 PHE cc_start: 0.6864 (p90) cc_final: 0.6358 (p90) REVERT: H 84 TYR cc_start: 0.7378 (p90) cc_final: 0.6941 (p90) REVERT: I 95 MET cc_start: 0.8897 (ppp) cc_final: 0.8448 (ppp) REVERT: I 104 MET cc_start: 0.8869 (ttt) cc_final: 0.7660 (ttt) REVERT: I 108 ILE cc_start: 0.9516 (mp) cc_final: 0.9075 (mp) REVERT: I 159 PHE cc_start: 0.8382 (t80) cc_final: 0.7926 (t80) REVERT: I 180 ASP cc_start: 0.8739 (m-30) cc_final: 0.8214 (m-30) REVERT: I 351 LYS cc_start: 0.9141 (tmtt) cc_final: 0.8896 (tptt) REVERT: I 370 GLU cc_start: 0.8153 (tp30) cc_final: 0.7671 (tp30) REVERT: I 383 PHE cc_start: 0.7435 (m-10) cc_final: 0.7136 (m-10) REVERT: I 423 ILE cc_start: 0.9541 (mm) cc_final: 0.9316 (mm) REVERT: I 479 TRP cc_start: 0.9063 (m-10) cc_final: 0.8430 (m-10) REVERT: I 494 LEU cc_start: 0.9349 (tp) cc_final: 0.8946 (tt) REVERT: J 574 LYS cc_start: 0.9269 (mmtp) cc_final: 0.8856 (mptt) REVERT: J 603 ILE cc_start: 0.8609 (mm) cc_final: 0.8370 (mm) REVERT: J 651 ASN cc_start: 0.8908 (m-40) cc_final: 0.8502 (m-40) REVERT: K 10 GLN cc_start: 0.7344 (mp10) cc_final: 0.7106 (mp10) REVERT: K 18 MET cc_start: 0.8601 (ppp) cc_final: 0.8381 (ppp) REVERT: K 36 TRP cc_start: 0.8483 (m100) cc_final: 0.7982 (m100) REVERT: K 39 LEU cc_start: 0.9463 (mm) cc_final: 0.9236 (mm) REVERT: K 82 LEU cc_start: 0.8777 (tp) cc_final: 0.8562 (tp) outliers start: 2 outliers final: 0 residues processed: 543 average time/residue: 0.2978 time to fit residues: 252.4690 Evaluate side-chains 426 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 141 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 45 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 204 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- 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 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 ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN ** J 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3717 r_free = 0.3717 target = 0.134074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111152 restraints weight = 49658.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114181 restraints weight = 32674.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116341 restraints weight = 24257.667| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20424 Z= 0.246 Angle : 0.892 18.235 27831 Z= 0.430 Chirality : 0.054 0.438 3198 Planarity : 0.005 0.072 3471 Dihedral : 10.292 75.040 3603 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.46 % Favored : 87.33 % Rotamer: Outliers : 0.23 % Allowed : 2.58 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.16), residues: 2424 helix: -0.20 (0.28), residues: 333 sheet: -1.09 (0.25), residues: 423 loop : -1.85 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 571 HIS 0.012 0.001 HIS I 374 PHE 0.022 0.003 PHE I 376 TYR 0.023 0.003 TYR A 191 ARG 0.008 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 9) link_NAG-ASN : angle 3.91885 ( 27) link_ALPHA1-6 : bond 0.00645 ( 12) link_ALPHA1-6 : angle 2.07939 ( 36) link_BETA1-4 : bond 0.02644 ( 18) link_BETA1-4 : angle 6.97082 ( 54) link_ALPHA1-3 : bond 0.01419 ( 9) link_ALPHA1-3 : angle 4.06445 ( 27) hydrogen bonds : bond 0.04524 ( 540) hydrogen bonds : angle 5.72447 ( 1458) SS BOND : bond 0.00563 ( 42) SS BOND : angle 1.43143 ( 84) covalent geometry : bond 0.00544 (20334) covalent geometry : angle 0.81535 (27603) *********************** 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 519 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 514 time to evaluate : 2.111 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 108 ILE cc_start: 0.9532 (mm) cc_final: 0.9247 (mm) REVERT: A 351 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8799 (tptt) REVERT: A 370 GLU cc_start: 0.8258 (tp30) cc_final: 0.7873 (tp30) REVERT: A 383 PHE cc_start: 0.7288 (m-10) cc_final: 0.7016 (m-10) REVERT: A 434 MET cc_start: 0.8453 (ppp) cc_final: 0.7934 (ppp) REVERT: A 494 LEU cc_start: 0.9452 (tp) cc_final: 0.9138 (tt) REVERT: B 574 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8483 (mttp) REVERT: B 588 ARG cc_start: 0.8944 (ttt180) cc_final: 0.8669 (ttt180) REVERT: C 36 TRP cc_start: 0.8499 (m100) cc_final: 0.8287 (m100) REVERT: C 46 GLU cc_start: 0.8401 (pp20) cc_final: 0.7927 (pp20) REVERT: C 80 LEU cc_start: 0.8836 (tt) cc_final: 0.8488 (tt) REVERT: C 89 VAL cc_start: 0.8465 (t) cc_final: 0.8186 (p) REVERT: D 81 PHE cc_start: 0.6984 (p90) cc_final: 0.6382 (p90) REVERT: D 103 GLN cc_start: 0.7720 (pt0) cc_final: 0.7324 (pp30) REVERT: E 102 ASP cc_start: 0.9113 (m-30) cc_final: 0.8789 (m-30) REVERT: E 279 ASN cc_start: 0.8105 (t0) cc_final: 0.7830 (p0) REVERT: E 301 ASN cc_start: 0.4064 (t0) cc_final: 0.3835 (t0) REVERT: E 348 GLU cc_start: 0.7561 (tt0) cc_final: 0.7247 (tt0) REVERT: E 369 MET cc_start: 0.7489 (mtt) cc_final: 0.7143 (mtt) REVERT: E 383 PHE cc_start: 0.7370 (m-10) cc_final: 0.7082 (m-10) REVERT: E 474 ASP cc_start: 0.8595 (t0) cc_final: 0.8257 (t0) REVERT: F 535 MET cc_start: 0.8592 (ttm) cc_final: 0.8251 (mmm) REVERT: F 574 LYS cc_start: 0.9224 (mmtp) cc_final: 0.8812 (mttp) REVERT: F 603 ILE cc_start: 0.8523 (mm) cc_final: 0.8272 (mm) REVERT: G 39 LEU cc_start: 0.9086 (mm) cc_final: 0.8871 (mm) REVERT: G 100 ASN cc_start: 0.9084 (p0) cc_final: 0.8623 (p0) REVERT: H 56 ILE cc_start: 0.8002 (mm) cc_final: 0.7750 (mm) REVERT: H 81 PHE cc_start: 0.7173 (p90) cc_final: 0.6610 (p90) REVERT: H 84 TYR cc_start: 0.7703 (p90) cc_final: 0.7169 (p90) REVERT: I 104 MET cc_start: 0.9025 (ttt) cc_final: 0.7964 (ttt) REVERT: I 108 ILE cc_start: 0.9528 (mp) cc_final: 0.9223 (mm) REVERT: I 180 ASP cc_start: 0.8896 (m-30) cc_final: 0.8654 (m-30) REVERT: I 308 ARG cc_start: 0.9165 (ttm-80) cc_final: 0.8866 (mmt90) REVERT: I 351 LYS cc_start: 0.9094 (tmtt) cc_final: 0.8816 (tptt) REVERT: I 370 GLU cc_start: 0.8195 (tp30) cc_final: 0.7809 (tp30) REVERT: I 474 ASP cc_start: 0.8437 (t0) cc_final: 0.8169 (t0) REVERT: I 479 TRP cc_start: 0.9213 (m-10) cc_final: 0.8520 (m-10) REVERT: I 494 LEU cc_start: 0.9423 (tp) cc_final: 0.9040 (tt) REVERT: J 651 ASN cc_start: 0.8908 (m-40) cc_final: 0.8606 (m-40) REVERT: K 10 GLN cc_start: 0.7463 (mp10) cc_final: 0.7005 (mp10) REVERT: K 18 MET cc_start: 0.8630 (ppp) cc_final: 0.8357 (ppp) REVERT: K 36 TRP cc_start: 0.8425 (m100) cc_final: 0.7965 (m100) REVERT: K 39 LEU cc_start: 0.9529 (mm) cc_final: 0.9208 (mm) REVERT: K 82 LEU cc_start: 0.8943 (tp) cc_final: 0.8665 (tp) REVERT: L 34 TYR cc_start: 0.8479 (m-10) cc_final: 0.8046 (m-10) outliers start: 5 outliers final: 0 residues processed: 518 average time/residue: 0.3045 time to fit residues: 247.9608 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 : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 193 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 195 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN J 575 GLN J 630 GLN K 58 ASN 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 = 0.3745 r_free = 0.3745 target = 0.136234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113431 restraints weight = 49098.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116574 restraints weight = 32137.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118808 restraints weight = 23666.521| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3033 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= 0.193 Angle : 0.848 17.379 27831 Z= 0.403 Chirality : 0.053 0.360 3198 Planarity : 0.005 0.071 3471 Dihedral : 9.880 73.327 3603 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.60 % Favored : 89.23 % Rotamer: Outliers : 0.19 % Allowed : 1.97 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.16), residues: 2424 helix: 0.17 (0.29), residues: 315 sheet: -1.05 (0.24), residues: 450 loop : -1.94 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 338 HIS 0.008 0.001 HIS G 102 PHE 0.022 0.002 PHE K 100D TYR 0.029 0.002 TYR J 586 ARG 0.007 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 9) link_NAG-ASN : angle 3.88980 ( 27) link_ALPHA1-6 : bond 0.00661 ( 12) link_ALPHA1-6 : angle 1.90680 ( 36) link_BETA1-4 : bond 0.02543 ( 18) link_BETA1-4 : angle 6.85124 ( 54) link_ALPHA1-3 : bond 0.01408 ( 9) link_ALPHA1-3 : angle 4.10152 ( 27) hydrogen bonds : bond 0.04217 ( 540) hydrogen bonds : angle 5.57224 ( 1458) SS BOND : bond 0.00417 ( 42) SS BOND : angle 1.40274 ( 84) covalent geometry : bond 0.00428 (20334) covalent geometry : angle 0.76905 (27603) *********************** 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 530 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 526 time to evaluate : 2.368 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 108 ILE cc_start: 0.9528 (mm) cc_final: 0.9261 (mm) REVERT: A 351 LYS cc_start: 0.8957 (tmtt) cc_final: 0.8731 (tptt) REVERT: A 370 GLU cc_start: 0.8229 (tp30) cc_final: 0.7869 (tp30) REVERT: A 383 PHE cc_start: 0.7273 (m-10) cc_final: 0.6973 (m-10) REVERT: A 434 MET cc_start: 0.8285 (ppp) cc_final: 0.7728 (ppp) REVERT: A 485 LYS cc_start: 0.8678 (mttt) cc_final: 0.8378 (mttt) REVERT: A 494 LEU cc_start: 0.9441 (tp) cc_final: 0.9125 (tt) REVERT: B 574 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8346 (mttp) REVERT: B 588 ARG cc_start: 0.8928 (ttt180) cc_final: 0.8580 (ttt180) REVERT: B 624 ASP cc_start: 0.7664 (m-30) cc_final: 0.7439 (m-30) REVERT: B 634 GLU cc_start: 0.8531 (mp0) cc_final: 0.8217 (mp0) REVERT: C 46 GLU cc_start: 0.8442 (pp20) cc_final: 0.8149 (pp20) REVERT: C 80 LEU cc_start: 0.8773 (tt) cc_final: 0.8473 (tt) REVERT: C 89 VAL cc_start: 0.8505 (t) cc_final: 0.8194 (p) REVERT: D 37 ARG cc_start: 0.8476 (tpt-90) cc_final: 0.8080 (tpt-90) REVERT: D 81 PHE cc_start: 0.6933 (p90) cc_final: 0.6349 (p90) REVERT: E 93 PHE cc_start: 0.8366 (m-10) cc_final: 0.8081 (m-80) REVERT: E 301 ASN cc_start: 0.4091 (t0) cc_final: 0.3838 (t0) REVERT: E 348 GLU cc_start: 0.7438 (tt0) cc_final: 0.7238 (tt0) REVERT: E 369 MET cc_start: 0.7533 (mtt) cc_final: 0.7212 (mtt) REVERT: E 383 PHE cc_start: 0.7313 (m-10) cc_final: 0.7013 (m-10) REVERT: E 474 ASP cc_start: 0.8602 (t0) cc_final: 0.8372 (t0) REVERT: E 485 LYS cc_start: 0.8897 (mttt) cc_final: 0.8565 (mttp) REVERT: F 574 LYS cc_start: 0.9211 (mmtp) cc_final: 0.8771 (mttp) REVERT: F 575 GLN cc_start: 0.8976 (mt0) cc_final: 0.8679 (pp30) REVERT: F 603 ILE cc_start: 0.8549 (mm) cc_final: 0.8344 (mm) REVERT: F 631 TRP cc_start: 0.7735 (t-100) cc_final: 0.7319 (t-100) REVERT: F 648 GLU cc_start: 0.9343 (pt0) cc_final: 0.9080 (pt0) REVERT: F 651 ASN cc_start: 0.8715 (m-40) cc_final: 0.8514 (m-40) REVERT: G 10 GLN cc_start: 0.7260 (mp10) cc_final: 0.6958 (pp30) REVERT: G 76 ASP cc_start: 0.7084 (t0) cc_final: 0.6622 (m-30) REVERT: G 96 LYS cc_start: 0.8473 (ptpt) cc_final: 0.7756 (ptpt) REVERT: G 100 ASN cc_start: 0.9229 (p0) cc_final: 0.8764 (p0) REVERT: H 56 ILE cc_start: 0.7961 (mm) cc_final: 0.7655 (mm) REVERT: H 81 PHE cc_start: 0.7110 (p90) cc_final: 0.6469 (p90) REVERT: H 84 TYR cc_start: 0.7720 (p90) cc_final: 0.7244 (p90) REVERT: I 97 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8687 (mptt) REVERT: I 104 MET cc_start: 0.8994 (ttt) cc_final: 0.7642 (ttt) REVERT: I 108 ILE cc_start: 0.9522 (mp) cc_final: 0.8978 (mp) REVERT: I 159 PHE cc_start: 0.8503 (t80) cc_final: 0.8216 (t80) REVERT: I 180 ASP cc_start: 0.8865 (m-30) cc_final: 0.8508 (m-30) REVERT: I 203 GLN cc_start: 0.8373 (tp40) cc_final: 0.8169 (tp40) REVERT: I 270 ILE cc_start: 0.8452 (mm) cc_final: 0.8228 (mm) REVERT: I 308 ARG cc_start: 0.9062 (ttm-80) cc_final: 0.8815 (mmt90) REVERT: I 351 LYS cc_start: 0.9083 (tmtt) cc_final: 0.8822 (tptt) REVERT: I 370 GLU cc_start: 0.8195 (tp30) cc_final: 0.7767 (tp30) REVERT: I 479 TRP cc_start: 0.9152 (m-10) cc_final: 0.8364 (m-10) REVERT: I 494 LEU cc_start: 0.9420 (tp) cc_final: 0.9086 (tt) REVERT: J 530 MET cc_start: 0.7732 (mmp) cc_final: 0.7523 (mmp) REVERT: J 603 ILE cc_start: 0.8683 (mm) cc_final: 0.8392 (mm) REVERT: J 651 ASN cc_start: 0.8940 (m-40) cc_final: 0.8624 (m-40) REVERT: K 10 GLN cc_start: 0.7371 (mp10) cc_final: 0.6982 (mp10) REVERT: K 18 MET cc_start: 0.8639 (ppp) cc_final: 0.8326 (ppp) REVERT: K 39 LEU cc_start: 0.9541 (mm) cc_final: 0.9121 (mm) REVERT: K 82 LEU cc_start: 0.8890 (tp) cc_final: 0.8574 (tp) REVERT: L 34 TYR cc_start: 0.8331 (m-10) cc_final: 0.7820 (m-10) outliers start: 4 outliers final: 0 residues processed: 528 average time/residue: 0.3451 time to fit residues: 284.7977 Evaluate side-chains 421 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 52 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 220 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 B 575 GLN ** E 195 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN J 577 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 = 0.3732 r_free = 0.3732 target = 0.135139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112018 restraints weight = 49605.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115230 restraints weight = 32259.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117484 restraints weight = 23626.092| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20424 Z= 0.208 Angle : 0.867 17.396 27831 Z= 0.415 Chirality : 0.053 0.370 3198 Planarity : 0.005 0.073 3471 Dihedral : 9.652 71.770 3603 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.09 % Favored : 87.75 % Rotamer: Outliers : 0.14 % Allowed : 1.64 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.16), residues: 2424 helix: 0.19 (0.29), residues: 312 sheet: -1.10 (0.24), residues: 486 loop : -1.96 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 36 HIS 0.005 0.001 HIS K 102 PHE 0.021 0.003 PHE K 100D TYR 0.027 0.002 TYR L 89 ARG 0.008 0.001 ARG I 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 9) link_NAG-ASN : angle 3.94399 ( 27) link_ALPHA1-6 : bond 0.00595 ( 12) link_ALPHA1-6 : angle 1.92857 ( 36) link_BETA1-4 : bond 0.02524 ( 18) link_BETA1-4 : angle 6.81472 ( 54) link_ALPHA1-3 : bond 0.01402 ( 9) link_ALPHA1-3 : angle 4.08602 ( 27) hydrogen bonds : bond 0.04294 ( 540) hydrogen bonds : angle 5.63631 ( 1458) SS BOND : bond 0.00451 ( 42) SS BOND : angle 1.38777 ( 84) covalent geometry : bond 0.00463 (20334) covalent geometry : angle 0.79076 (27603) *********************** 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 511 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 508 time to evaluate : 4.862 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 370 GLU cc_start: 0.8202 (tp30) cc_final: 0.7848 (tp30) REVERT: A 383 PHE cc_start: 0.7201 (m-10) cc_final: 0.6909 (m-10) REVERT: A 434 MET cc_start: 0.8424 (ppp) cc_final: 0.8003 (ppp) REVERT: A 485 LYS cc_start: 0.8733 (mttt) cc_final: 0.8524 (mttt) REVERT: A 494 LEU cc_start: 0.9470 (tp) cc_final: 0.9144 (tt) REVERT: B 574 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8326 (mttp) REVERT: B 588 ARG cc_start: 0.8926 (ttt180) cc_final: 0.8574 (ttt180) REVERT: B 624 ASP cc_start: 0.7753 (m-30) cc_final: 0.7527 (m-30) REVERT: C 46 GLU cc_start: 0.8462 (pp20) cc_final: 0.8121 (pp20) REVERT: C 82 LEU cc_start: 0.8681 (pp) cc_final: 0.8374 (pp) REVERT: C 89 VAL cc_start: 0.8496 (t) cc_final: 0.8056 (p) REVERT: D 37 ARG cc_start: 0.8483 (tpt-90) cc_final: 0.8088 (tpt-90) REVERT: D 81 PHE cc_start: 0.7036 (p90) cc_final: 0.6446 (p90) REVERT: E 121 LYS cc_start: 0.9451 (mppt) cc_final: 0.9199 (mmtm) REVERT: E 369 MET cc_start: 0.7550 (mtt) cc_final: 0.7197 (mtt) REVERT: E 383 PHE cc_start: 0.7395 (m-10) cc_final: 0.7071 (m-10) REVERT: E 460 THR cc_start: 0.7784 (p) cc_final: 0.7568 (p) REVERT: F 574 LYS cc_start: 0.9208 (mmtp) cc_final: 0.8828 (mptt) REVERT: F 603 ILE cc_start: 0.8588 (mm) cc_final: 0.8363 (mm) REVERT: F 631 TRP cc_start: 0.7605 (t-100) cc_final: 0.7326 (t-100) REVERT: F 648 GLU cc_start: 0.9326 (pt0) cc_final: 0.9047 (pt0) REVERT: F 651 ASN cc_start: 0.8697 (m-40) cc_final: 0.8496 (m-40) REVERT: G 76 ASP cc_start: 0.7113 (t0) cc_final: 0.6628 (m-30) REVERT: G 96 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7741 (tppt) REVERT: G 97 ASN cc_start: 0.9187 (p0) cc_final: 0.8960 (p0) REVERT: G 100 ASN cc_start: 0.9255 (p0) cc_final: 0.8808 (p0) REVERT: H 31 LEU cc_start: 0.8740 (mm) cc_final: 0.8523 (mm) REVERT: H 56 ILE cc_start: 0.7860 (mm) cc_final: 0.7614 (mm) REVERT: H 81 PHE cc_start: 0.7256 (p90) cc_final: 0.6599 (p90) REVERT: H 84 TYR cc_start: 0.7805 (p90) cc_final: 0.7368 (p90) REVERT: I 97 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8644 (mptt) REVERT: I 104 MET cc_start: 0.8999 (ttt) cc_final: 0.7640 (ttt) REVERT: I 108 ILE cc_start: 0.9536 (mp) cc_final: 0.8925 (mp) REVERT: I 159 PHE cc_start: 0.8474 (t80) cc_final: 0.8239 (t80) REVERT: I 180 ASP cc_start: 0.8878 (m-30) cc_final: 0.8521 (m-30) REVERT: I 270 ILE cc_start: 0.8506 (mm) cc_final: 0.8306 (mm) REVERT: I 308 ARG cc_start: 0.9068 (ttm-80) cc_final: 0.8733 (mmt90) REVERT: I 351 LYS cc_start: 0.9081 (tmtt) cc_final: 0.8796 (tptt) REVERT: I 370 GLU cc_start: 0.8203 (tp30) cc_final: 0.7774 (tp30) REVERT: I 479 TRP cc_start: 0.9154 (m-10) cc_final: 0.8319 (m-10) REVERT: I 494 LEU cc_start: 0.9428 (tp) cc_final: 0.8894 (tt) REVERT: J 603 ILE cc_start: 0.8484 (mm) cc_final: 0.8242 (mm) REVERT: J 651 ASN cc_start: 0.8938 (m-40) cc_final: 0.8657 (m-40) REVERT: K 10 GLN cc_start: 0.7440 (mp10) cc_final: 0.7034 (mp10) REVERT: K 18 MET cc_start: 0.8645 (ppp) cc_final: 0.8331 (ppp) REVERT: K 39 LEU cc_start: 0.9573 (mm) cc_final: 0.9143 (mm) REVERT: K 82 LEU cc_start: 0.8927 (tp) cc_final: 0.8590 (tp) REVERT: L 34 TYR cc_start: 0.8362 (m-10) cc_final: 0.8080 (m-10) outliers start: 3 outliers final: 0 residues processed: 510 average time/residue: 0.3773 time to fit residues: 299.9237 Evaluate side-chains 416 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 129 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 152 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 543 ASN G 64 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** 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** J 575 GLN K 100AASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111930 restraints weight = 49968.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114991 restraints weight = 32630.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117108 restraints weight = 24065.640| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20424 Z= 0.237 Angle : 0.910 17.686 27831 Z= 0.441 Chirality : 0.055 0.395 3198 Planarity : 0.005 0.074 3471 Dihedral : 9.622 69.947 3603 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.21 % Favored : 87.58 % Rotamer: Outliers : 0.09 % Allowed : 1.36 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.16), residues: 2424 helix: -0.06 (0.29), residues: 312 sheet: -1.36 (0.24), residues: 480 loop : -1.97 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 338 HIS 0.007 0.001 HIS G 102 PHE 0.022 0.003 PHE L 81 TYR 0.026 0.002 TYR J 586 ARG 0.008 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00722 ( 9) link_NAG-ASN : angle 4.11197 ( 27) link_ALPHA1-6 : bond 0.00531 ( 12) link_ALPHA1-6 : angle 1.94491 ( 36) link_BETA1-4 : bond 0.02435 ( 18) link_BETA1-4 : angle 6.87095 ( 54) link_ALPHA1-3 : bond 0.01369 ( 9) link_ALPHA1-3 : angle 4.09000 ( 27) hydrogen bonds : bond 0.04562 ( 540) hydrogen bonds : angle 5.79753 ( 1458) SS BOND : bond 0.00474 ( 42) SS BOND : angle 1.41744 ( 84) covalent geometry : bond 0.00530 (20334) covalent geometry : angle 0.83637 (27603) *********************** 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 495 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9318 (mppt) cc_final: 0.9083 (mmtt) REVERT: A 370 GLU cc_start: 0.8231 (tp30) cc_final: 0.7810 (tp30) REVERT: A 383 PHE cc_start: 0.7225 (m-10) cc_final: 0.6849 (m-10) REVERT: A 485 LYS cc_start: 0.8682 (mttt) cc_final: 0.8479 (mttt) REVERT: A 494 LEU cc_start: 0.9480 (tp) cc_final: 0.9217 (tt) REVERT: B 574 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8258 (mttp) REVERT: B 588 ARG cc_start: 0.8916 (ttt180) cc_final: 0.8566 (ttt180) REVERT: B 624 ASP cc_start: 0.7823 (m-30) cc_final: 0.7591 (m-30) REVERT: C 82 LEU cc_start: 0.8740 (pp) cc_final: 0.8438 (pp) REVERT: C 89 VAL cc_start: 0.8455 (t) cc_final: 0.8060 (p) REVERT: D 13 LEU cc_start: 0.8706 (pt) cc_final: 0.8458 (pt) REVERT: D 37 ARG cc_start: 0.8509 (tpt-90) cc_final: 0.8132 (tpt-90) REVERT: D 81 PHE cc_start: 0.7110 (p90) cc_final: 0.6431 (p90) REVERT: E 121 LYS cc_start: 0.9445 (mppt) cc_final: 0.9176 (mmtm) REVERT: E 369 MET cc_start: 0.7607 (mtt) cc_final: 0.7238 (mtt) REVERT: E 377 ASN cc_start: 0.7867 (t0) cc_final: 0.7545 (t0) REVERT: E 383 PHE cc_start: 0.7387 (m-10) cc_final: 0.6998 (m-10) REVERT: F 574 LYS cc_start: 0.9215 (mmtp) cc_final: 0.8824 (mptt) REVERT: F 648 GLU cc_start: 0.9315 (pt0) cc_final: 0.8832 (pp20) REVERT: F 651 ASN cc_start: 0.8739 (m-40) cc_final: 0.8516 (m-40) REVERT: G 76 ASP cc_start: 0.7066 (t0) cc_final: 0.6660 (m-30) REVERT: G 96 LYS cc_start: 0.8061 (ptpt) cc_final: 0.7701 (tppp) REVERT: G 97 ASN cc_start: 0.9235 (p0) cc_final: 0.9033 (p0) REVERT: G 100 ASN cc_start: 0.9264 (p0) cc_final: 0.8794 (p0) REVERT: H 47 TYR cc_start: 0.7227 (m-80) cc_final: 0.6682 (m-80) REVERT: H 56 ILE cc_start: 0.7868 (mm) cc_final: 0.7648 (mm) REVERT: H 81 PHE cc_start: 0.7179 (p90) cc_final: 0.6531 (p90) REVERT: H 94 GLU cc_start: 0.8756 (pt0) cc_final: 0.8275 (pm20) REVERT: I 104 MET cc_start: 0.8991 (ttt) cc_final: 0.7655 (ttt) REVERT: I 108 ILE cc_start: 0.9540 (mp) cc_final: 0.8982 (mp) REVERT: I 180 ASP cc_start: 0.8874 (m-30) cc_final: 0.8493 (m-30) REVERT: I 308 ARG cc_start: 0.9090 (ttm-80) cc_final: 0.8731 (mmt90) REVERT: I 351 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8749 (tptt) REVERT: I 369 MET cc_start: 0.7539 (mtt) cc_final: 0.7333 (mtt) REVERT: I 370 GLU cc_start: 0.8166 (tp30) cc_final: 0.7771 (tp30) REVERT: I 479 TRP cc_start: 0.9172 (m-10) cc_final: 0.8362 (m-10) REVERT: I 494 LEU cc_start: 0.9482 (tp) cc_final: 0.9244 (tt) REVERT: J 651 ASN cc_start: 0.8960 (m-40) cc_final: 0.8678 (m-40) REVERT: K 18 MET cc_start: 0.8668 (ppp) cc_final: 0.8374 (ppp) REVERT: K 39 LEU cc_start: 0.9446 (mm) cc_final: 0.9201 (mm) outliers start: 2 outliers final: 0 residues processed: 493 average time/residue: 0.2946 time to fit residues: 226.2682 Evaluate side-chains 405 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 20 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 58 ASN C 64 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 543 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 ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114272 restraints weight = 48648.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117497 restraints weight = 31290.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119729 restraints weight = 22848.428| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20424 Z= 0.173 Angle : 0.867 17.539 27831 Z= 0.415 Chirality : 0.054 0.411 3198 Planarity : 0.005 0.072 3471 Dihedral : 9.316 68.644 3603 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.52 % Favored : 89.27 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.16), residues: 2424 helix: 0.02 (0.30), residues: 312 sheet: -1.28 (0.24), residues: 480 loop : -1.88 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 631 HIS 0.010 0.001 HIS K 102 PHE 0.018 0.002 PHE I 210 TYR 0.043 0.002 TYR D 85 ARG 0.005 0.000 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 9) link_NAG-ASN : angle 3.98655 ( 27) link_ALPHA1-6 : bond 0.00622 ( 12) link_ALPHA1-6 : angle 1.79531 ( 36) link_BETA1-4 : bond 0.02554 ( 18) link_BETA1-4 : angle 6.78769 ( 54) link_ALPHA1-3 : bond 0.01413 ( 9) link_ALPHA1-3 : angle 4.20542 ( 27) hydrogen bonds : bond 0.04340 ( 540) hydrogen bonds : angle 5.58686 ( 1458) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.30346 ( 84) covalent geometry : bond 0.00380 (20334) covalent geometry : angle 0.79132 (27603) ********************** 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 511 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 510 time to evaluate : 2.611 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 121 LYS cc_start: 0.9353 (mppt) cc_final: 0.9127 (mmtt) REVERT: A 369 MET cc_start: 0.7467 (mtm) cc_final: 0.7125 (mtt) REVERT: A 370 GLU cc_start: 0.8153 (tp30) cc_final: 0.7801 (tp30) REVERT: A 383 PHE cc_start: 0.7190 (m-10) cc_final: 0.6870 (m-10) REVERT: B 574 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8220 (mttp) REVERT: B 588 ARG cc_start: 0.8895 (ttt180) cc_final: 0.8518 (ttt180) REVERT: B 624 ASP cc_start: 0.7779 (m-30) cc_final: 0.7535 (m-30) REVERT: C 82 LEU cc_start: 0.8671 (pp) cc_final: 0.8408 (pp) REVERT: D 13 LEU cc_start: 0.8628 (pt) cc_final: 0.8082 (mp) REVERT: D 37 ARG cc_start: 0.8497 (tpt-90) cc_final: 0.8072 (tpt-90) REVERT: D 81 PHE cc_start: 0.7012 (p90) cc_final: 0.6384 (p90) REVERT: E 49 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8643 (tmtt) REVERT: E 93 PHE cc_start: 0.8380 (m-10) cc_final: 0.8047 (m-80) REVERT: E 121 LYS cc_start: 0.9450 (mppt) cc_final: 0.9159 (mmtm) REVERT: E 154 MET cc_start: 0.3486 (tpt) cc_final: 0.3001 (tpt) REVERT: E 369 MET cc_start: 0.7565 (mtt) cc_final: 0.7201 (mtt) REVERT: E 383 PHE cc_start: 0.7373 (m-10) cc_final: 0.7035 (m-10) REVERT: E 423 ILE cc_start: 0.9505 (mm) cc_final: 0.9304 (mm) REVERT: E 485 LYS cc_start: 0.9060 (mttt) cc_final: 0.8591 (mmtp) REVERT: F 574 LYS cc_start: 0.9219 (mmtp) cc_final: 0.8890 (mptt) REVERT: F 651 ASN cc_start: 0.8687 (m-40) cc_final: 0.8437 (m-40) REVERT: G 76 ASP cc_start: 0.7098 (t0) cc_final: 0.6650 (m-30) REVERT: G 96 LYS cc_start: 0.8088 (ptpt) cc_final: 0.7670 (tppt) REVERT: G 97 ASN cc_start: 0.9235 (p0) cc_final: 0.9027 (p0) REVERT: G 100 ASN cc_start: 0.9286 (p0) cc_final: 0.8798 (p0) REVERT: H 4 LEU cc_start: 0.7573 (tp) cc_final: 0.7329 (tp) REVERT: H 56 ILE cc_start: 0.7755 (mm) cc_final: 0.7472 (mm) REVERT: H 60 PHE cc_start: 0.8957 (m-80) cc_final: 0.8457 (m-80) REVERT: H 81 PHE cc_start: 0.7293 (p90) cc_final: 0.6641 (p90) REVERT: H 84 TYR cc_start: 0.7790 (p90) cc_final: 0.7395 (p90) REVERT: H 94 GLU cc_start: 0.8895 (pt0) cc_final: 0.8261 (pm20) REVERT: I 35 TRP cc_start: 0.7482 (m-10) cc_final: 0.7037 (m-10) REVERT: I 95 MET cc_start: 0.8758 (ppp) cc_final: 0.8206 (ppp) REVERT: I 97 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8590 (mptt) REVERT: I 104 MET cc_start: 0.8966 (ttt) cc_final: 0.7703 (ttt) REVERT: I 108 ILE cc_start: 0.9564 (mp) cc_final: 0.8981 (mp) REVERT: I 159 PHE cc_start: 0.8508 (t80) cc_final: 0.8251 (t80) REVERT: I 180 ASP cc_start: 0.8772 (m-30) cc_final: 0.8383 (m-30) REVERT: I 270 ILE cc_start: 0.8342 (mm) cc_final: 0.8127 (mm) REVERT: I 308 ARG cc_start: 0.9083 (ttm-80) cc_final: 0.8723 (mmt90) REVERT: I 351 LYS cc_start: 0.9015 (tmtt) cc_final: 0.8621 (tptt) REVERT: I 370 GLU cc_start: 0.8128 (tp30) cc_final: 0.7686 (tp30) REVERT: I 383 PHE cc_start: 0.7662 (m-10) cc_final: 0.7373 (m-10) REVERT: I 479 TRP cc_start: 0.9087 (m-10) cc_final: 0.8276 (m-10) REVERT: I 494 LEU cc_start: 0.9427 (tp) cc_final: 0.9177 (tt) REVERT: J 530 MET cc_start: 0.7673 (mmp) cc_final: 0.7419 (mmp) REVERT: J 651 ASN cc_start: 0.8905 (m-40) cc_final: 0.8632 (m-40) REVERT: K 18 MET cc_start: 0.8652 (ppp) cc_final: 0.8355 (ppp) REVERT: L 47 TYR cc_start: 0.7205 (m-80) cc_final: 0.6601 (m-80) REVERT: L 60 PHE cc_start: 0.8560 (m-80) cc_final: 0.8280 (m-80) outliers start: 1 outliers final: 1 residues processed: 510 average time/residue: 0.3993 time to fit residues: 326.4575 Evaluate side-chains 408 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 172 optimal weight: 0.3980 chunk 48 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 58 ASN C 64 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 543 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** J 575 GLN ** J 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117098 restraints weight = 50206.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120410 restraints weight = 32366.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122748 restraints weight = 23579.322| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3610 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= 0.148 Angle : 0.840 17.775 27831 Z= 0.395 Chirality : 0.053 0.425 3198 Planarity : 0.004 0.067 3471 Dihedral : 8.959 67.511 3603 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.61 % Favored : 90.18 % Rotamer: Outliers : 0.05 % Allowed : 0.23 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.16), residues: 2424 helix: 0.17 (0.30), residues: 312 sheet: -1.23 (0.24), residues: 480 loop : -1.75 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 36 HIS 0.004 0.001 HIS C 102 PHE 0.033 0.002 PHE K 100D TYR 0.029 0.002 TYR F 586 ARG 0.010 0.000 ARG I 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 9) link_NAG-ASN : angle 3.88812 ( 27) link_ALPHA1-6 : bond 0.00657 ( 12) link_ALPHA1-6 : angle 1.72037 ( 36) link_BETA1-4 : bond 0.02610 ( 18) link_BETA1-4 : angle 6.74097 ( 54) link_ALPHA1-3 : bond 0.01425 ( 9) link_ALPHA1-3 : angle 4.26817 ( 27) hydrogen bonds : bond 0.03960 ( 540) hydrogen bonds : angle 5.35965 ( 1458) SS BOND : bond 0.00350 ( 42) SS BOND : angle 1.36334 ( 84) covalent geometry : bond 0.00319 (20334) covalent geometry : angle 0.76184 (27603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6886.63 seconds wall clock time: 124 minutes 54.80 seconds (7494.80 seconds total)