Starting phenix.real_space_refine on Tue May 20 11:51:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8san_40274/05_2025/8san_40274_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8san_40274/05_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_40274/05_2025/8san_40274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8san_40274/05_2025/8san_40274.map" model { file = "/net/cci-nas-00/data/ceres_data/8san_40274/05_2025/8san_40274_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8san_40274/05_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-5687/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: 12.33, per 1000 atoms: 0.62 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: 5.80 Conformation dependent library (CDL) restraints added in 2.5 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: 2.81 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: 6.79 Time building geometry restraints manager: 6.63 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: 0.320 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: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.480 Find NCS groups from input model: 0.630 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.670 ------------------------------------------------------------------------------- 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 : 2.288 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: 0.3099 time to fit residues: 264.1230 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 : 2.399 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116146 restraints weight = 49626.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119420 restraints weight = 31919.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121761 restraints weight = 23184.006| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 7.51937 ( 54) link_ALPHA1-3 : bond 0.01306 ( 9) link_ALPHA1-3 : angle 4.24793 ( 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 : 2.152 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: 0.8211 (tp30) cc_final: 0.8001 (tm-30) REVERT: A 102 ASP cc_start: 0.8895 (m-30) cc_final: 0.8554 (m-30) REVERT: A 177 TYR cc_start: 0.5396 (m-80) cc_final: 0.4647 (m-80) REVERT: A 180 ASP cc_start: 0.8830 (m-30) cc_final: 0.8529 (m-30) REVERT: A 216 HIS cc_start: 0.8378 (m-70) cc_final: 0.8118 (m90) REVERT: A 370 GLU cc_start: 0.8198 (tp30) cc_final: 0.7827 (tp30) REVERT: B 574 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8310 (mttp) REVERT: C 39 LEU cc_start: 0.9443 (mm) cc_final: 0.9194 (mm) REVERT: C 51 LEU cc_start: 0.8388 (tt) cc_final: 0.8005 (mp) REVERT: C 69 MET cc_start: 0.8649 (ptm) cc_final: 0.8073 (ptm) REVERT: D 34 TYR cc_start: 0.8114 (m-10) cc_final: 0.7872 (m-10) REVERT: D 81 PHE cc_start: 0.6912 (p90) cc_final: 0.6360 (p90) REVERT: D 103 GLN cc_start: 0.7766 (pt0) cc_final: 0.7347 (pp30) REVERT: E 102 ASP cc_start: 0.9037 (m-30) cc_final: 0.8719 (m-30) REVERT: E 104 MET cc_start: 0.8600 (tpp) cc_final: 0.8347 (mmt) REVERT: E 217 TYR cc_start: 0.6681 (m-10) cc_final: 0.4472 (m-10) REVERT: E 426 MET cc_start: 0.8712 (ptp) cc_final: 0.8425 (tpt) REVERT: E 460 THR cc_start: 0.8243 (p) cc_final: 0.8022 (p) REVERT: F 651 ASN cc_start: 0.8799 (m-40) cc_final: 0.8571 (m-40) REVERT: G 36 TRP cc_start: 0.8350 (m100) cc_final: 0.7791 (m100) REVERT: G 89 VAL cc_start: 0.8752 (t) cc_final: 0.8380 (p) REVERT: G 96 LYS cc_start: 0.8525 (ptpt) cc_final: 0.8264 (ptpt) REVERT: G 100 TYR cc_start: 0.8327 (t80) cc_final: 0.8008 (t80) REVERT: H 84 TYR cc_start: 0.7457 (p90) cc_final: 0.6875 (p90) REVERT: I 159 PHE cc_start: 0.8523 (t80) cc_final: 0.8163 (t80) REVERT: I 180 ASP cc_start: 0.8865 (m-30) cc_final: 0.8340 (m-30) REVERT: I 351 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8898 (tptt) REVERT: I 370 GLU cc_start: 0.8243 (tp30) cc_final: 0.7850 (tp30) REVERT: I 426 MET cc_start: 0.8850 (ptp) cc_final: 0.8275 (tpt) REVERT: I 474 ASP cc_start: 0.8488 (t0) cc_final: 0.8282 (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: 0.8183 (m100) REVERT: K 48 MET cc_start: 0.8803 (tpp) cc_final: 0.8311 (tpp) REVERT: K 82 LEU cc_start: 0.8764 (tp) cc_final: 0.8469 (tp) REVERT: K 96 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8180 (ptpt) outliers start: 4 outliers final: 1 residues processed: 537 average time/residue: 0.2874 time to fit residues: 238.3434 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 : 2.444 ------------------------------------------------------------------------------- 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: 9.9990 chunk 39 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 70 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 229 ASN A 478 ASN B 577 GLN E 478 ASN F 543 ASN G 58 ASN H 103 GLN I 156 ASN J 575 GLN ** 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 = 0.3742 r_free = 0.3742 target = 0.135567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112710 restraints weight = 49570.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115838 restraints weight = 31937.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118097 restraints weight = 23436.949| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20424 Z= 0.243 Angle : 0.892 18.209 27831 Z= 0.427 Chirality : 0.053 0.333 3198 Planarity : 0.005 0.066 3471 Dihedral : 13.393 96.110 3603 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.76 % Favored : 88.00 % Rotamer: Outliers : 0.23 % Allowed : 4.27 % Favored : 95.50 % 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: -2.07 (0.16), residues: 2424 helix: 0.30 (0.29), residues: 315 sheet: -1.15 (0.23), residues: 480 loop : -1.89 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 33 HIS 0.005 0.001 HIS C 102 PHE 0.035 0.003 PHE A 53 TYR 0.026 0.003 TYR A 177 ARG 0.011 0.001 ARG I 192 Details of bonding type rmsd link_NAG-ASN : bond 0.01048 ( 9) link_NAG-ASN : angle 3.93003 ( 27) link_ALPHA1-6 : bond 0.00727 ( 12) link_ALPHA1-6 : angle 2.04810 ( 36) link_BETA1-4 : bond 0.02723 ( 18) link_BETA1-4 : angle 7.25002 ( 54) link_ALPHA1-3 : bond 0.01293 ( 9) link_ALPHA1-3 : angle 4.23440 ( 27) hydrogen bonds : bond 0.05033 ( 540) hydrogen bonds : angle 5.97493 ( 1458) SS BOND : bond 0.00833 ( 42) SS BOND : angle 1.39994 ( 84) covalent geometry : bond 0.00530 (20334) covalent geometry : angle 0.80926 (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 501 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 496 time to evaluate : 2.271 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 154 MET cc_start: 0.2510 (tpt) cc_final: 0.2162 (tpt) REVERT: A 177 TYR cc_start: 0.5991 (m-80) cc_final: 0.4992 (m-80) REVERT: A 351 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8774 (tptt) REVERT: A 369 MET cc_start: 0.7768 (mtt) cc_final: 0.7496 (mtt) REVERT: A 370 GLU cc_start: 0.8319 (tp30) cc_final: 0.7800 (tp30) REVERT: A 383 PHE cc_start: 0.7372 (m-10) cc_final: 0.7114 (m-10) REVERT: A 434 MET cc_start: 0.8154 (ppp) cc_final: 0.7724 (ppp) REVERT: B 571 TRP cc_start: 0.7159 (m-10) cc_final: 0.6265 (m-10) REVERT: B 591 GLN cc_start: 0.9410 (tp40) cc_final: 0.9145 (tp-100) REVERT: C 39 LEU cc_start: 0.9479 (mm) cc_final: 0.9120 (mm) REVERT: C 48 MET cc_start: 0.7950 (tpp) cc_final: 0.7558 (tpp) REVERT: C 51 LEU cc_start: 0.8619 (tt) cc_final: 0.8219 (mp) REVERT: D 81 PHE cc_start: 0.6955 (p90) cc_final: 0.6439 (p90) REVERT: D 103 GLN cc_start: 0.7772 (pt0) cc_final: 0.7417 (pp30) REVERT: E 121 LYS cc_start: 0.9413 (mppt) cc_final: 0.9168 (mmtm) REVERT: E 369 MET cc_start: 0.7513 (mtt) cc_final: 0.7230 (mtt) REVERT: E 383 PHE cc_start: 0.7462 (m-10) cc_final: 0.7130 (m-10) REVERT: E 426 MET cc_start: 0.8795 (ptp) cc_final: 0.8400 (tpt) REVERT: E 474 ASP cc_start: 0.8560 (t0) cc_final: 0.8340 (t0) REVERT: F 574 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8969 (mmtp) REVERT: G 36 TRP cc_start: 0.8455 (m100) cc_final: 0.7630 (m100) REVERT: G 100 TYR cc_start: 0.8356 (t80) cc_final: 0.7964 (t80) REVERT: G 100 ASN cc_start: 0.8952 (p0) cc_final: 0.8638 (p0) REVERT: H 37 ARG cc_start: 0.8362 (tpt-90) cc_final: 0.8159 (tpt-90) REVERT: H 56 ILE cc_start: 0.8076 (mm) cc_final: 0.7856 (mm) REVERT: H 84 TYR cc_start: 0.7598 (p90) cc_final: 0.7012 (p90) REVERT: I 159 PHE cc_start: 0.8436 (t80) cc_final: 0.8187 (t80) REVERT: I 180 ASP cc_start: 0.8967 (m-30) cc_final: 0.8520 (m-30) REVERT: I 351 LYS cc_start: 0.9124 (tmtt) cc_final: 0.8850 (tptt) REVERT: I 370 GLU cc_start: 0.8170 (tp30) cc_final: 0.7839 (tp30) REVERT: I 426 MET cc_start: 0.9021 (ptp) cc_final: 0.8236 (tpt) REVERT: J 530 MET cc_start: 0.7929 (mmm) cc_final: 0.7703 (mmt) REVERT: J 574 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9117 (mmtm) REVERT: J 603 ILE cc_start: 0.8841 (mm) cc_final: 0.8543 (mm) REVERT: J 651 ASN cc_start: 0.8792 (m-40) cc_final: 0.8531 (m-40) REVERT: K 18 MET cc_start: 0.8557 (ppp) cc_final: 0.8315 (ppp) REVERT: K 36 TRP cc_start: 0.8665 (m100) cc_final: 0.8290 (m100) REVERT: K 39 LEU cc_start: 0.9274 (mm) cc_final: 0.8864 (mm) REVERT: K 48 MET cc_start: 0.8805 (tpp) cc_final: 0.8407 (tpp) REVERT: K 82 LEU cc_start: 0.8848 (tp) cc_final: 0.8614 (tp) outliers start: 5 outliers final: 0 residues processed: 499 average time/residue: 0.3015 time to fit residues: 232.1017 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 : 2.154 ------------------------------------------------------------------------------- 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: 5.9990 chunk 228 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN E 216 HIS ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN G 58 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 GLN I 300 ASN ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN ** 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 = 0.3726 r_free = 0.3726 target = 0.134505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111597 restraints weight = 49959.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114658 restraints weight = 32768.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116853 restraints weight = 24172.708| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2551 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= 0.218 Angle : 0.869 17.627 27831 Z= 0.415 Chirality : 0.053 0.369 3198 Planarity : 0.005 0.069 3471 Dihedral : 12.247 85.571 3603 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.59 % Favored : 88.20 % Rotamer: Outliers : 0.14 % Allowed : 5.16 % Favored : 94.70 % 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: -2.15 (0.16), residues: 2424 helix: 0.33 (0.30), residues: 315 sheet: -1.36 (0.22), residues: 507 loop : -1.92 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 36 HIS 0.006 0.001 HIS C 102 PHE 0.019 0.002 PHE K 100D TYR 0.021 0.002 TYR A 217 ARG 0.008 0.001 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00932 ( 9) link_NAG-ASN : angle 4.01154 ( 27) link_ALPHA1-6 : bond 0.00719 ( 12) link_ALPHA1-6 : angle 2.02409 ( 36) link_BETA1-4 : bond 0.02565 ( 18) link_BETA1-4 : angle 7.07295 ( 54) link_ALPHA1-3 : bond 0.01340 ( 9) link_ALPHA1-3 : angle 4.07709 ( 27) hydrogen bonds : bond 0.04558 ( 540) hydrogen bonds : angle 5.73700 ( 1458) SS BOND : bond 0.00483 ( 42) SS BOND : angle 1.30629 ( 84) covalent geometry : bond 0.00480 (20334) covalent geometry : angle 0.78749 (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 517 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 514 time to evaluate : 2.290 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 351 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8770 (tptt) REVERT: A 369 MET cc_start: 0.7729 (mtt) cc_final: 0.7229 (mtt) REVERT: A 370 GLU cc_start: 0.8291 (tp30) cc_final: 0.7813 (tp30) REVERT: A 383 PHE cc_start: 0.7319 (m-10) cc_final: 0.7113 (m-10) REVERT: A 434 MET cc_start: 0.8340 (ppp) cc_final: 0.7863 (ppp) REVERT: B 574 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8362 (mttp) REVERT: B 588 ARG cc_start: 0.8851 (ttt180) cc_final: 0.8648 (ttt180) REVERT: C 37 ILE cc_start: 0.8742 (mt) cc_final: 0.8483 (tp) REVERT: C 39 LEU cc_start: 0.9495 (mm) cc_final: 0.9071 (mm) REVERT: D 81 PHE cc_start: 0.7004 (p90) cc_final: 0.6470 (p90) REVERT: D 98 GLN cc_start: 0.8063 (tp40) cc_final: 0.7810 (pt0) REVERT: D 103 GLN cc_start: 0.7804 (pt0) cc_final: 0.7313 (pp30) REVERT: E 348 GLU cc_start: 0.7538 (tt0) cc_final: 0.7163 (tt0) REVERT: E 369 MET cc_start: 0.7592 (mtt) cc_final: 0.7252 (mtt) REVERT: E 377 ASN cc_start: 0.7702 (t0) cc_final: 0.7468 (t0) REVERT: E 383 PHE cc_start: 0.7335 (m-10) cc_final: 0.7133 (m-10) REVERT: E 474 ASP cc_start: 0.8183 (t0) cc_final: 0.7977 (t0) REVERT: F 574 LYS cc_start: 0.9227 (mmtp) cc_final: 0.8804 (mptt) REVERT: F 575 GLN cc_start: 0.9087 (mt0) cc_final: 0.8737 (mp10) REVERT: F 603 ILE cc_start: 0.8536 (mm) cc_final: 0.8333 (mm) REVERT: F 631 TRP cc_start: 0.7877 (t-100) cc_final: 0.7429 (t-100) REVERT: F 651 ASN cc_start: 0.8749 (m-40) cc_final: 0.8543 (m-40) REVERT: G 36 TRP cc_start: 0.8530 (m100) cc_final: 0.7581 (m100) REVERT: G 100 TYR cc_start: 0.8321 (t80) cc_final: 0.8121 (t80) REVERT: G 100 ASN cc_start: 0.9068 (p0) cc_final: 0.8728 (p0) REVERT: H 56 ILE cc_start: 0.8093 (mm) cc_final: 0.7867 (mm) REVERT: H 84 TYR cc_start: 0.7740 (p90) cc_final: 0.7151 (p90) REVERT: I 104 MET cc_start: 0.9017 (ttt) cc_final: 0.7908 (ttt) REVERT: I 108 ILE cc_start: 0.9535 (mm) cc_final: 0.9268 (mm) REVERT: I 308 ARG cc_start: 0.9149 (ttm-80) cc_final: 0.8795 (mmt90) REVERT: I 351 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8842 (tptt) REVERT: I 370 GLU cc_start: 0.8282 (tp30) cc_final: 0.7937 (tp30) REVERT: I 426 MET cc_start: 0.8943 (ptp) cc_final: 0.8175 (tpt) REVERT: I 474 ASP cc_start: 0.8502 (t0) cc_final: 0.8175 (t0) REVERT: I 479 TRP cc_start: 0.9136 (m-10) cc_final: 0.8492 (m-10) REVERT: J 574 LYS cc_start: 0.9268 (mmtp) cc_final: 0.9027 (mmtm) REVERT: J 603 ILE cc_start: 0.8665 (mm) cc_final: 0.8448 (mm) REVERT: J 651 ASN cc_start: 0.8922 (m-40) cc_final: 0.8562 (m-40) REVERT: K 18 MET cc_start: 0.8601 (ppp) cc_final: 0.8310 (ppp) REVERT: K 36 TRP cc_start: 0.8573 (m100) cc_final: 0.7941 (m100) REVERT: K 39 LEU cc_start: 0.9497 (mm) cc_final: 0.9079 (mm) REVERT: K 48 MET cc_start: 0.8750 (tpp) cc_final: 0.8434 (tpp) REVERT: K 82 LEU cc_start: 0.8917 (tp) cc_final: 0.8639 (tp) REVERT: L 31 LEU cc_start: 0.8797 (mm) cc_final: 0.8584 (mm) REVERT: L 34 TYR cc_start: 0.8245 (m-10) cc_final: 0.7921 (m-10) REVERT: L 47 TYR cc_start: 0.7549 (m-80) cc_final: 0.7346 (m-80) outliers start: 3 outliers final: 0 residues processed: 516 average time/residue: 0.2936 time to fit residues: 233.9885 Evaluate side-chains 408 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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: 10.0000 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 212 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN G 58 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112792 restraints weight = 49582.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115950 restraints weight = 32147.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118234 restraints weight = 23558.567| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2752 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= 0.192 Angle : 0.859 17.861 27831 Z= 0.407 Chirality : 0.053 0.372 3198 Planarity : 0.005 0.069 3471 Dihedral : 11.424 77.742 3603 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.43 % Favored : 88.37 % Rotamer: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % 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: -2.23 (0.16), residues: 2424 helix: -0.07 (0.28), residues: 333 sheet: -1.34 (0.22), residues: 507 loop : -1.94 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 623 HIS 0.009 0.001 HIS I 374 PHE 0.019 0.002 PHE K 100D TYR 0.033 0.002 TYR B 586 ARG 0.007 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 9) link_NAG-ASN : angle 4.03699 ( 27) link_ALPHA1-6 : bond 0.00741 ( 12) link_ALPHA1-6 : angle 1.98263 ( 36) link_BETA1-4 : bond 0.02546 ( 18) link_BETA1-4 : angle 7.19873 ( 54) link_ALPHA1-3 : bond 0.01379 ( 9) link_ALPHA1-3 : angle 4.12495 ( 27) hydrogen bonds : bond 0.04324 ( 540) hydrogen bonds : angle 5.64162 ( 1458) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.41806 ( 84) covalent geometry : bond 0.00419 (20334) covalent geometry : angle 0.77346 (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 525 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 524 time to evaluate : 2.186 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 159 PHE cc_start: 0.8587 (t80) cc_final: 0.8368 (t80) REVERT: A 351 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8765 (tptt) REVERT: A 370 GLU cc_start: 0.8221 (tp30) cc_final: 0.7748 (tp30) REVERT: A 383 PHE cc_start: 0.7356 (m-10) cc_final: 0.7030 (m-10) REVERT: A 434 MET cc_start: 0.8287 (ppp) cc_final: 0.7818 (ppp) REVERT: B 574 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8335 (mttp) REVERT: C 13 LYS cc_start: 0.9361 (mmtp) cc_final: 0.9084 (mmtp) REVERT: C 82 LEU cc_start: 0.8726 (pp) cc_final: 0.8525 (pp) REVERT: C 89 VAL cc_start: 0.8611 (t) cc_final: 0.8155 (p) REVERT: D 81 PHE cc_start: 0.6948 (p90) cc_final: 0.6348 (p90) REVERT: D 103 GLN cc_start: 0.7741 (pt0) cc_final: 0.7351 (pp30) REVERT: E 348 GLU cc_start: 0.7369 (tt0) cc_final: 0.7046 (tt0) REVERT: E 369 MET cc_start: 0.7551 (mtt) cc_final: 0.7240 (mtt) REVERT: E 383 PHE cc_start: 0.7413 (m-10) cc_final: 0.7174 (m-10) REVERT: E 474 ASP cc_start: 0.8550 (t0) cc_final: 0.8256 (t0) REVERT: F 530 MET cc_start: 0.8514 (pmm) cc_final: 0.7703 (ptt) REVERT: F 574 LYS cc_start: 0.9227 (mmtp) cc_final: 0.8636 (mttp) REVERT: F 575 GLN cc_start: 0.8972 (mt0) cc_final: 0.8663 (tm-30) REVERT: F 603 ILE cc_start: 0.8640 (mm) cc_final: 0.8327 (mm) REVERT: F 626 MET cc_start: 0.6382 (tpp) cc_final: 0.5946 (tpt) REVERT: F 631 TRP cc_start: 0.7785 (t-100) cc_final: 0.7471 (t-100) REVERT: F 648 GLU cc_start: 0.9336 (pt0) cc_final: 0.9098 (pt0) REVERT: G 76 ASP cc_start: 0.7049 (t0) cc_final: 0.6526 (m-30) REVERT: G 100 TYR cc_start: 0.8361 (t80) cc_final: 0.8140 (t80) REVERT: G 100 ASN cc_start: 0.9135 (p0) cc_final: 0.8752 (p0) REVERT: H 56 ILE cc_start: 0.8084 (mm) cc_final: 0.7820 (mm) REVERT: H 81 PHE cc_start: 0.7068 (p90) cc_final: 0.6434 (p90) REVERT: H 84 TYR cc_start: 0.7733 (p90) cc_final: 0.7263 (p90) REVERT: I 104 MET cc_start: 0.9085 (ttt) cc_final: 0.8062 (ttt) REVERT: I 108 ILE cc_start: 0.9543 (mm) cc_final: 0.9288 (mm) REVERT: I 159 PHE cc_start: 0.8500 (t80) cc_final: 0.8176 (t80) REVERT: I 180 ASP cc_start: 0.8862 (m-30) cc_final: 0.8466 (m-30) REVERT: I 308 ARG cc_start: 0.9130 (ttm-80) cc_final: 0.8765 (mmt90) REVERT: I 351 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8853 (tptt) REVERT: I 370 GLU cc_start: 0.8182 (tp30) cc_final: 0.7746 (tp30) REVERT: I 479 TRP cc_start: 0.9146 (m-10) cc_final: 0.8539 (m-10) REVERT: I 485 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8347 (mtmt) REVERT: I 494 LEU cc_start: 0.9399 (tp) cc_final: 0.8897 (tt) REVERT: J 603 ILE cc_start: 0.8830 (mm) cc_final: 0.8392 (mm) REVERT: J 651 ASN cc_start: 0.8916 (m-40) cc_final: 0.8530 (m-40) REVERT: K 18 MET cc_start: 0.8590 (ppp) cc_final: 0.8329 (ppp) REVERT: K 36 TRP cc_start: 0.8516 (m100) cc_final: 0.7965 (m100) REVERT: K 82 LEU cc_start: 0.8860 (tp) cc_final: 0.8641 (tp) REVERT: L 31 LEU cc_start: 0.8707 (mm) cc_final: 0.8495 (mm) REVERT: L 34 TYR cc_start: 0.8361 (m-10) cc_final: 0.7762 (m-10) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.2948 time to fit residues: 239.1716 Evaluate side-chains 414 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 204 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN E 195 ASN E 478 ASN F 543 ASN G 58 ASN G 64 GLN H 36 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111554 restraints weight = 49546.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114658 restraints weight = 32356.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116863 restraints weight = 23909.132| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2996 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= 0.214 Angle : 0.870 17.515 27831 Z= 0.416 Chirality : 0.053 0.381 3198 Planarity : 0.005 0.071 3471 Dihedral : 10.515 74.161 3603 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.38 % Favored : 87.42 % Rotamer: Outliers : 0.19 % Allowed : 3.00 % Favored : 96.81 % 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: -2.23 (0.16), residues: 2424 helix: 0.27 (0.29), residues: 312 sheet: -1.24 (0.24), residues: 456 loop : -2.03 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 623 HIS 0.006 0.001 HIS A 72 PHE 0.023 0.003 PHE C 100D TYR 0.030 0.002 TYR B 586 ARG 0.007 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00759 ( 9) link_NAG-ASN : angle 3.92240 ( 27) link_ALPHA1-6 : bond 0.00695 ( 12) link_ALPHA1-6 : angle 1.98661 ( 36) link_BETA1-4 : bond 0.02608 ( 18) link_BETA1-4 : angle 6.96270 ( 54) link_ALPHA1-3 : bond 0.01397 ( 9) link_ALPHA1-3 : angle 4.11759 ( 27) hydrogen bonds : bond 0.04381 ( 540) hydrogen bonds : angle 5.69296 ( 1458) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.51956 ( 84) covalent geometry : bond 0.00472 (20334) covalent geometry : angle 0.78997 (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 514 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 510 time to evaluate : 2.323 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 108 ILE cc_start: 0.9531 (mm) cc_final: 0.9222 (mm) REVERT: A 370 GLU cc_start: 0.8177 (tp30) cc_final: 0.7751 (tp30) REVERT: A 383 PHE cc_start: 0.7261 (m-10) cc_final: 0.7006 (m-10) REVERT: A 434 MET cc_start: 0.8494 (ppp) cc_final: 0.7977 (ppp) REVERT: B 574 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8441 (mttp) REVERT: C 39 LEU cc_start: 0.9478 (mm) cc_final: 0.9193 (mm) REVERT: C 46 GLU cc_start: 0.8468 (pp20) cc_final: 0.8101 (pp20) REVERT: C 89 VAL cc_start: 0.8588 (t) cc_final: 0.8306 (p) REVERT: D 81 PHE cc_start: 0.7053 (p90) cc_final: 0.6435 (p90) REVERT: E 121 LYS cc_start: 0.9452 (mppt) cc_final: 0.9171 (mmtm) REVERT: E 348 GLU cc_start: 0.7537 (tt0) cc_final: 0.7272 (tt0) REVERT: E 369 MET cc_start: 0.7653 (mtt) cc_final: 0.7305 (mtt) REVERT: E 383 PHE cc_start: 0.7398 (m-10) cc_final: 0.7092 (m-10) REVERT: E 474 ASP cc_start: 0.8532 (t0) cc_final: 0.8236 (t0) REVERT: F 530 MET cc_start: 0.8509 (pmm) cc_final: 0.8103 (ptm) REVERT: F 574 LYS cc_start: 0.9234 (mmtp) cc_final: 0.8689 (mttp) REVERT: F 575 GLN cc_start: 0.9060 (mt0) cc_final: 0.8701 (tm-30) REVERT: F 603 ILE cc_start: 0.8514 (mm) cc_final: 0.8271 (mm) REVERT: F 626 MET cc_start: 0.6431 (tpp) cc_final: 0.6021 (tpt) REVERT: F 631 TRP cc_start: 0.7696 (t-100) cc_final: 0.7481 (t-100) REVERT: F 648 GLU cc_start: 0.9345 (pt0) cc_final: 0.9069 (pt0) REVERT: F 651 ASN cc_start: 0.8729 (m-40) cc_final: 0.8527 (m-40) REVERT: G 76 ASP cc_start: 0.7154 (t0) cc_final: 0.6637 (m-30) REVERT: G 100 ASN cc_start: 0.9110 (p0) cc_final: 0.8741 (p0) REVERT: H 56 ILE cc_start: 0.8039 (mm) cc_final: 0.7759 (mm) REVERT: H 81 PHE cc_start: 0.7195 (p90) cc_final: 0.6599 (p90) REVERT: I 104 MET cc_start: 0.9108 (ttt) cc_final: 0.8030 (ttt) REVERT: I 108 ILE cc_start: 0.9534 (mm) cc_final: 0.9287 (mm) REVERT: I 159 PHE cc_start: 0.8401 (t80) cc_final: 0.8165 (t80) REVERT: I 180 ASP cc_start: 0.8877 (m-30) cc_final: 0.8517 (m-30) REVERT: I 308 ARG cc_start: 0.9080 (ttm-80) cc_final: 0.8785 (mmt90) REVERT: I 351 LYS cc_start: 0.9106 (tmtt) cc_final: 0.8857 (tptt) REVERT: I 370 GLU cc_start: 0.8162 (tp30) cc_final: 0.7771 (tp30) REVERT: I 474 ASP cc_start: 0.8460 (t0) cc_final: 0.8212 (t0) REVERT: I 479 TRP cc_start: 0.9179 (m-10) cc_final: 0.8555 (m-10) REVERT: I 494 LEU cc_start: 0.9449 (tp) cc_final: 0.9206 (tt) REVERT: J 651 ASN cc_start: 0.8981 (m-40) cc_final: 0.8695 (m-40) REVERT: K 10 GLN cc_start: 0.7655 (mp10) cc_final: 0.7153 (mp10) REVERT: K 18 MET cc_start: 0.8680 (ppp) cc_final: 0.8353 (ppp) REVERT: K 36 TRP cc_start: 0.8485 (m100) cc_final: 0.7876 (m100) REVERT: K 39 LEU cc_start: 0.9527 (mm) cc_final: 0.9151 (mm) REVERT: K 82 LEU cc_start: 0.8948 (tp) cc_final: 0.8642 (tp) REVERT: L 31 LEU cc_start: 0.8749 (mm) cc_final: 0.8535 (mm) REVERT: L 34 TYR cc_start: 0.8383 (m-10) cc_final: 0.7923 (m-10) outliers start: 4 outliers final: 0 residues processed: 513 average time/residue: 0.2972 time to fit residues: 236.6317 Evaluate side-chains 412 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN 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 G 58 ASN ** H 103 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.136519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113659 restraints weight = 48795.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116811 restraints weight = 31600.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119072 restraints weight = 23228.527| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20424 Z= 0.176 Angle : 0.843 17.462 27831 Z= 0.401 Chirality : 0.052 0.361 3198 Planarity : 0.005 0.071 3471 Dihedral : 10.000 72.879 3603 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.06 % Favored : 88.74 % Rotamer: Outliers : 0.14 % Allowed : 1.97 % Favored : 97.89 % 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: -2.19 (0.16), residues: 2424 helix: 0.19 (0.29), residues: 312 sheet: -1.26 (0.23), residues: 486 loop : -1.97 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 36 HIS 0.009 0.001 HIS G 102 PHE 0.025 0.002 PHE K 100D TYR 0.028 0.002 TYR B 586 ARG 0.015 0.001 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 9) link_NAG-ASN : angle 3.94156 ( 27) link_ALPHA1-6 : bond 0.00698 ( 12) link_ALPHA1-6 : angle 1.89176 ( 36) link_BETA1-4 : bond 0.02574 ( 18) link_BETA1-4 : angle 6.86202 ( 54) link_ALPHA1-3 : bond 0.01441 ( 9) link_ALPHA1-3 : angle 4.14059 ( 27) hydrogen bonds : bond 0.04131 ( 540) hydrogen bonds : angle 5.54550 ( 1458) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.34813 ( 84) covalent geometry : bond 0.00387 (20334) covalent geometry : angle 0.76323 (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 513 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 510 time to evaluate : 2.266 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 283 ILE cc_start: 0.9324 (mt) cc_final: 0.9044 (mt) REVERT: A 369 MET cc_start: 0.7481 (mtm) cc_final: 0.7113 (mtt) REVERT: A 370 GLU cc_start: 0.8215 (tp30) cc_final: 0.7791 (tp30) REVERT: A 383 PHE cc_start: 0.7287 (m-10) cc_final: 0.6918 (m-10) REVERT: A 434 MET cc_start: 0.8400 (ppp) cc_final: 0.7873 (ppp) REVERT: B 574 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8372 (mttp) REVERT: B 603 ILE cc_start: 0.8838 (mm) cc_final: 0.8613 (mm) REVERT: B 624 ASP cc_start: 0.7747 (m-30) cc_final: 0.7494 (m-30) REVERT: C 28 GLU cc_start: 0.8273 (pm20) cc_final: 0.8071 (pm20) REVERT: C 31 ASP cc_start: 0.8662 (m-30) cc_final: 0.8339 (m-30) REVERT: C 82 LEU cc_start: 0.8648 (pp) cc_final: 0.8415 (pp) REVERT: D 81 PHE cc_start: 0.6991 (p90) cc_final: 0.6382 (p90) REVERT: E 121 LYS cc_start: 0.9447 (mppt) cc_final: 0.9119 (mmtm) REVERT: E 369 MET cc_start: 0.7560 (mtt) cc_final: 0.7169 (mtt) REVERT: E 383 PHE cc_start: 0.7382 (m-10) cc_final: 0.7078 (m-10) REVERT: E 426 MET cc_start: 0.8744 (ptp) cc_final: 0.7540 (tpt) REVERT: E 460 THR cc_start: 0.7774 (p) cc_final: 0.7487 (p) REVERT: E 474 ASP cc_start: 0.8547 (t0) cc_final: 0.8305 (t0) REVERT: F 530 MET cc_start: 0.8527 (pmm) cc_final: 0.8125 (ptp) REVERT: F 574 LYS cc_start: 0.9229 (mmtp) cc_final: 0.8727 (mttp) REVERT: F 575 GLN cc_start: 0.8983 (mt0) cc_final: 0.8692 (tm-30) REVERT: F 603 ILE cc_start: 0.8532 (mm) cc_final: 0.8304 (mm) REVERT: F 648 GLU cc_start: 0.9302 (pt0) cc_final: 0.8914 (pt0) REVERT: F 651 ASN cc_start: 0.8695 (m-40) cc_final: 0.8456 (m-40) REVERT: G 76 ASP cc_start: 0.7111 (t0) cc_final: 0.6631 (m-30) REVERT: G 96 LYS cc_start: 0.8502 (ptpt) cc_final: 0.7953 (mttt) REVERT: G 100 ASN cc_start: 0.9147 (p0) cc_final: 0.8696 (p0) REVERT: H 47 TYR cc_start: 0.7146 (m-80) cc_final: 0.6042 (m-80) REVERT: H 56 ILE cc_start: 0.7977 (mm) cc_final: 0.7743 (mm) REVERT: H 73 ILE cc_start: 0.9509 (mm) cc_final: 0.9236 (mp) REVERT: H 81 PHE cc_start: 0.7065 (p90) cc_final: 0.6413 (p90) REVERT: H 84 TYR cc_start: 0.7786 (p90) cc_final: 0.7277 (p90) REVERT: I 104 MET cc_start: 0.9125 (ttt) cc_final: 0.8118 (ttt) REVERT: I 108 ILE cc_start: 0.9538 (mm) cc_final: 0.9305 (mm) REVERT: I 159 PHE cc_start: 0.8399 (t80) cc_final: 0.8141 (t80) REVERT: I 180 ASP cc_start: 0.8874 (m-30) cc_final: 0.8523 (m-30) REVERT: I 203 GLN cc_start: 0.8627 (tp40) cc_final: 0.8415 (tp40) REVERT: I 270 ILE cc_start: 0.8427 (mm) cc_final: 0.8176 (mm) REVERT: I 308 ARG cc_start: 0.8999 (ttm-80) cc_final: 0.8579 (mmt90) REVERT: I 351 LYS cc_start: 0.9091 (tmtt) cc_final: 0.8815 (tptt) REVERT: I 370 GLU cc_start: 0.8104 (tp30) cc_final: 0.7708 (tp30) REVERT: I 383 PHE cc_start: 0.7657 (m-10) cc_final: 0.7328 (m-10) REVERT: I 423 ILE cc_start: 0.9578 (mm) cc_final: 0.9371 (mm) REVERT: I 479 TRP cc_start: 0.9136 (m-10) cc_final: 0.8608 (m-10) REVERT: I 494 LEU cc_start: 0.9434 (tp) cc_final: 0.9133 (tt) REVERT: J 651 ASN cc_start: 0.8962 (m-40) cc_final: 0.8661 (m-40) REVERT: K 10 GLN cc_start: 0.7497 (mp10) cc_final: 0.7042 (mp10) REVERT: K 18 MET cc_start: 0.8598 (ppp) cc_final: 0.8313 (ppp) REVERT: K 39 LEU cc_start: 0.9534 (mm) cc_final: 0.9156 (mm) REVERT: K 82 LEU cc_start: 0.8911 (tp) cc_final: 0.8562 (tp) REVERT: L 34 TYR cc_start: 0.8305 (m-10) cc_final: 0.7953 (m-10) outliers start: 3 outliers final: 0 residues processed: 512 average time/residue: 0.3183 time to fit residues: 252.4940 Evaluate side-chains 412 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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: 0.2980 chunk 72 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 164 optimal weight: 30.0000 chunk 85 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN ** 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 ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** 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 = 0.3795 r_free = 0.3795 target = 0.139581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117112 restraints weight = 49479.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120258 restraints weight = 32121.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122472 restraints weight = 23613.502| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20424 Z= 0.153 Angle : 0.826 17.480 27831 Z= 0.389 Chirality : 0.052 0.390 3198 Planarity : 0.004 0.069 3471 Dihedral : 9.506 71.856 3603 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.44 % Favored : 89.36 % Rotamer: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.69 % 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: -2.04 (0.16), residues: 2424 helix: 0.26 (0.30), residues: 312 sheet: -1.19 (0.23), residues: 486 loop : -1.83 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 36 HIS 0.005 0.001 HIS E 249 PHE 0.026 0.002 PHE C 100D TYR 0.025 0.002 TYR B 586 ARG 0.008 0.001 ARG D 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 9) link_NAG-ASN : angle 3.80390 ( 27) link_ALPHA1-6 : bond 0.00698 ( 12) link_ALPHA1-6 : angle 1.80978 ( 36) link_BETA1-4 : bond 0.02593 ( 18) link_BETA1-4 : angle 6.78596 ( 54) link_ALPHA1-3 : bond 0.01486 ( 9) link_ALPHA1-3 : angle 4.21677 ( 27) hydrogen bonds : bond 0.03951 ( 540) hydrogen bonds : angle 5.39917 ( 1458) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.23284 ( 84) covalent geometry : bond 0.00333 (20334) covalent geometry : angle 0.74620 (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 507 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 505 time to evaluate : 2.317 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: A 93 PHE cc_start: 0.8332 (m-10) cc_final: 0.8083 (m-10) REVERT: A 108 ILE cc_start: 0.9481 (mm) cc_final: 0.9011 (mm) REVERT: A 121 LYS cc_start: 0.9302 (mmtm) cc_final: 0.9098 (mmtt) REVERT: A 369 MET cc_start: 0.7413 (mtm) cc_final: 0.6851 (mtt) REVERT: A 370 GLU cc_start: 0.8062 (tp30) cc_final: 0.7747 (tp30) REVERT: A 383 PHE cc_start: 0.7154 (m-10) cc_final: 0.6854 (m-10) REVERT: B 624 ASP cc_start: 0.7731 (m-30) cc_final: 0.7483 (m-30) REVERT: C 100 TYR cc_start: 0.7738 (t80) cc_final: 0.7308 (t80) REVERT: D 13 LEU cc_start: 0.8553 (pt) cc_final: 0.8062 (mp) REVERT: D 81 PHE cc_start: 0.6889 (p90) cc_final: 0.6265 (p90) REVERT: E 93 PHE cc_start: 0.8347 (m-10) cc_final: 0.8056 (m-80) REVERT: E 121 LYS cc_start: 0.9454 (mppt) cc_final: 0.9191 (mmtm) REVERT: E 369 MET cc_start: 0.7489 (mtt) cc_final: 0.7126 (mtt) REVERT: E 426 MET cc_start: 0.8730 (ptp) cc_final: 0.7619 (tpt) REVERT: E 474 ASP cc_start: 0.8629 (t0) cc_final: 0.8281 (t0) REVERT: F 530 MET cc_start: 0.8479 (pmm) cc_final: 0.8192 (ptp) REVERT: F 574 LYS cc_start: 0.9219 (mmtp) cc_final: 0.8818 (mttp) REVERT: F 575 GLN cc_start: 0.9093 (mt0) cc_final: 0.8676 (tm-30) REVERT: F 603 ILE cc_start: 0.8532 (mm) cc_final: 0.8286 (mm) REVERT: F 626 MET cc_start: 0.6331 (tpp) cc_final: 0.6112 (tpp) REVERT: F 631 TRP cc_start: 0.7522 (t-100) cc_final: 0.7138 (t-100) REVERT: F 651 ASN cc_start: 0.8708 (m-40) cc_final: 0.8496 (m-40) REVERT: G 35 ASN cc_start: 0.8758 (m-40) cc_final: 0.8336 (p0) REVERT: G 76 ASP cc_start: 0.7094 (t0) cc_final: 0.6683 (m-30) REVERT: G 96 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8289 (ttmt) REVERT: G 100 ASN cc_start: 0.9127 (p0) cc_final: 0.8664 (p0) REVERT: H 56 ILE cc_start: 0.7969 (mm) cc_final: 0.7720 (mm) REVERT: H 84 TYR cc_start: 0.7814 (p90) cc_final: 0.7406 (p90) REVERT: H 94 GLU cc_start: 0.8397 (pm20) cc_final: 0.8149 (pm20) REVERT: H 95 PHE cc_start: 0.8424 (m-10) cc_final: 0.8037 (m-10) REVERT: I 97 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8619 (mptt) REVERT: I 104 MET cc_start: 0.9110 (ttt) cc_final: 0.8103 (ttt) REVERT: I 108 ILE cc_start: 0.9533 (mm) cc_final: 0.9277 (mm) REVERT: I 180 ASP cc_start: 0.8727 (m-30) cc_final: 0.8331 (m-30) REVERT: I 203 GLN cc_start: 0.8629 (tp40) cc_final: 0.8339 (tp40) REVERT: I 308 ARG cc_start: 0.9034 (ttm-80) cc_final: 0.8634 (mmt90) REVERT: I 351 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8777 (tptt) REVERT: I 369 MET cc_start: 0.7615 (mtt) cc_final: 0.7412 (mtt) REVERT: I 370 GLU cc_start: 0.8123 (tp30) cc_final: 0.7910 (tp30) REVERT: I 383 PHE cc_start: 0.7580 (m-10) cc_final: 0.7279 (m-10) REVERT: I 423 ILE cc_start: 0.9572 (mm) cc_final: 0.9344 (mm) REVERT: I 426 MET cc_start: 0.8868 (ptp) cc_final: 0.7727 (tpt) REVERT: I 479 TRP cc_start: 0.9102 (m-10) cc_final: 0.8551 (m-10) REVERT: I 485 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8159 (mtmm) REVERT: J 651 ASN cc_start: 0.8940 (m-40) cc_final: 0.8605 (m-40) REVERT: K 10 GLN cc_start: 0.7483 (mp10) cc_final: 0.7028 (mp10) REVERT: K 18 MET cc_start: 0.8576 (ppp) cc_final: 0.8370 (ppp) REVERT: K 36 TRP cc_start: 0.8404 (m100) cc_final: 0.7957 (m100) REVERT: K 39 LEU cc_start: 0.9519 (mm) cc_final: 0.9121 (mm) REVERT: K 101 GLU cc_start: 0.8348 (mp0) cc_final: 0.8112 (mp0) REVERT: L 13 LEU cc_start: 0.8325 (mt) cc_final: 0.8095 (mt) REVERT: L 34 TYR cc_start: 0.8169 (m-10) cc_final: 0.7859 (m-10) REVERT: L 47 TYR cc_start: 0.7355 (m-80) cc_final: 0.7153 (m-80) outliers start: 2 outliers final: 0 residues processed: 505 average time/residue: 0.3011 time to fit residues: 237.0390 Evaluate side-chains 420 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.0737 > 50: distance: 12 - 13: 3.646 distance: 13 - 14: 9.892 distance: 13 - 16: 12.212 distance: 14 - 15: 10.667 distance: 14 - 21: 9.163 distance: 16 - 17: 5.773 distance: 17 - 18: 9.977 distance: 18 - 19: 9.693 distance: 18 - 20: 17.287 distance: 21 - 22: 8.307 distance: 22 - 23: 12.432 distance: 22 - 25: 7.009 distance: 23 - 24: 9.641 distance: 23 - 29: 12.250 distance: 25 - 26: 5.556 distance: 26 - 27: 16.247 distance: 27 - 28: 6.126 distance: 29 - 30: 12.362 distance: 30 - 31: 13.631 distance: 30 - 33: 11.457 distance: 31 - 32: 8.218 distance: 31 - 38: 9.832 distance: 33 - 34: 8.862 distance: 34 - 35: 19.227 distance: 35 - 36: 7.052 distance: 36 - 37: 21.360 distance: 38 - 39: 9.678 distance: 39 - 40: 25.473 distance: 39 - 42: 16.764 distance: 40 - 41: 34.358 distance: 40 - 47: 31.029 distance: 42 - 43: 25.057 distance: 43 - 44: 14.936 distance: 44 - 45: 17.669 distance: 45 - 46: 36.318 distance: 47 - 48: 21.971 distance: 47 - 53: 20.024 distance: 48 - 49: 10.290 distance: 48 - 51: 7.409 distance: 49 - 50: 12.383 distance: 49 - 54: 15.973 distance: 51 - 52: 4.462 distance: 54 - 55: 25.865 distance: 55 - 56: 34.471 distance: 56 - 57: 30.113 distance: 56 - 58: 16.192 distance: 58 - 59: 11.720 distance: 59 - 60: 11.640 distance: 59 - 62: 19.596 distance: 60 - 61: 17.588 distance: 60 - 67: 5.903 distance: 62 - 63: 16.651 distance: 63 - 64: 16.369 distance: 64 - 65: 5.545 distance: 64 - 66: 16.071 distance: 67 - 68: 7.556 distance: 68 - 69: 10.735 distance: 69 - 70: 9.274 distance: 69 - 73: 10.199 distance: 71 - 72: 8.861 distance: 73 - 74: 3.299 distance: 73 - 121: 10.080 distance: 74 - 75: 5.591 distance: 74 - 77: 8.344 distance: 76 - 118: 6.541 distance: 77 - 78: 8.042 distance: 78 - 79: 8.591 distance: 79 - 80: 9.240 distance: 81 - 82: 6.352 distance: 82 - 83: 4.174 distance: 82 - 85: 5.818 distance: 83 - 84: 3.789 distance: 83 - 92: 5.176 distance: 85 - 86: 5.854 distance: 86 - 87: 6.244 distance: 87 - 88: 8.754 distance: 88 - 89: 4.831 distance: 89 - 90: 9.785 distance: 89 - 91: 7.430