Starting phenix.real_space_refine on Tue Aug 26 15:21:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgv_43225/08_2025/8vgv_43225_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgv_43225/08_2025/8vgv_43225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgv_43225/08_2025/8vgv_43225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgv_43225/08_2025/8vgv_43225.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgv_43225/08_2025/8vgv_43225_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgv_43225/08_2025/8vgv_43225_neut_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.212 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: 5 Type Number sf(0) Gaussians S 141 5.16 5 C 12291 2.51 5 N 3330 2.21 5 O 3870 1.98 5 H 18767 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38399 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7149 Classifications: {'peptide': 462} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2053 Classifications: {'peptide': 132} Modifications used: {'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1932 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1555 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 7148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7148 Classifications: {'peptide': 462} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "F" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2053 Classifications: {'peptide': 132} Modifications used: {'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1932 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "H" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1555 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 7149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7149 Classifications: {'peptide': 462} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "J" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2053 Classifications: {'peptide': 132} Modifications used: {'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "K" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1932 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1555 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" 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: "N" 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: "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: 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: "R" 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 Time building chain proxies: 8.36, per 1000 atoms: 0.22 Number of scatterers: 38399 At special positions: 0 Unit cell: (160.92, 155.52, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 O 3870 8.00 N 3330 7.00 C 12291 6.00 H 18767 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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 201 " - pdb=" SG CYS A 433 " 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 B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 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 F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 101 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " 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 J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 91 " - pdb=" SG CYS L 101 " 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 ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " 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-ASN " NAG M 1 " - " ASN A 332 " " NAG N 1 " - " ASN A 301 " " NAG O 1 " - " ASN E 332 " " NAG P 1 " - " ASN E 301 " " NAG Q 1 " - " ASN I 332 " " NAG R 1 " - " ASN I 301 " Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4566 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 43 sheets defined 24.0% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.758A pdb=" N ASN A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.637A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.925A pdb=" N THR A 138 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.682A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 425 through 432 removed outlier: 3.931A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 430 " --> pdb=" O TRP A 427 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.033A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 519 Processing helix chain 'B' and resid 528 through 534 removed outlier: 4.104A pdb=" N ALA B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.292A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 572 through 597 removed outlier: 4.101A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.536A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.611A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.548A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.572A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'E' and resid 63 through 68 Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.513A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.558A pdb=" N LYS E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.137A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.919A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 520 Processing helix chain 'F' and resid 528 through 534 removed outlier: 3.980A pdb=" N ALA F 532 " --> pdb=" O SER F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.183A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 569 through 571 No H-bonds generated for 'chain 'F' and resid 569 through 571' Processing helix chain 'F' and resid 572 through 597 removed outlier: 4.157A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.619A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.636A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.603A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.664A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 Processing helix chain 'I' and resid 63 through 68 Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.630A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 353 removed outlier: 4.049A pdb=" N HIS I 352 " --> pdb=" O GLU I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 425 through 432 removed outlier: 4.100A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL I 430 " --> pdb=" O TRP I 427 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY I 431 " --> pdb=" O GLN I 428 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 481 removed outlier: 4.163A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 519 removed outlier: 3.941A pdb=" N PHE J 519 " --> pdb=" O ILE J 515 " (cutoff:3.500A) Processing helix chain 'J' and resid 528 through 534 removed outlier: 4.130A pdb=" N ALA J 532 " --> pdb=" O SER J 528 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 4.037A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 543 through 545 No H-bonds generated for 'chain 'J' and resid 543 through 545' Processing helix chain 'J' and resid 569 through 571 No H-bonds generated for 'chain 'J' and resid 569 through 571' Processing helix chain 'J' and resid 572 through 597 removed outlier: 4.072A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA J 582 " --> pdb=" O ALA J 578 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU J 592 " --> pdb=" O ARG J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 626 removed outlier: 3.921A pdb=" N ASP J 624 " --> pdb=" O SER J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.631A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 3.825A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.599A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 removed outlier: 5.133A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.956A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.570A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 175 removed outlier: 3.597A pdb=" N SER A 132 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.760A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.497A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.480A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 305 through 309 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.889A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.562A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB5, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB6, first strand: chain 'E' and resid 495 through 498 removed outlier: 5.154A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.071A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.701A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC2, first strand: chain 'E' and resid 133 through 136 removed outlier: 5.077A pdb=" N ALA E 134 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 139 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.733A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.605A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.782A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.267A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.267A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.782A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 302 through 309 removed outlier: 6.976A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.812A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.598A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD2, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'I' and resid 494 through 498 removed outlier: 6.907A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.052A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AD6, first strand: chain 'I' and resid 91 through 93 removed outlier: 3.550A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 167 through 175 removed outlier: 7.406A pdb=" N MET I 152 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA I 134 " --> pdb=" O MET I 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER I 132 " --> pdb=" O ASN I 154 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.791A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.454A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 11.132A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.063A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.779A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.691A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.494A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 305 through 308 Processing sheet with id=AE3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.769A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.536A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE7, first strand: chain 'L' and resid 18 through 23 724 hydrogen bonds defined for protein. 1863 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: 11.08 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18755 1.03 - 1.23: 803 1.23 - 1.43: 7872 1.43 - 1.63: 11197 1.63 - 1.83: 192 Bond restraints: 38819 Sorted by residual: bond pdb=" N GLU A 32 " pdb=" H1 GLU A 32 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N GLU I 32 " pdb=" H1 GLU I 32 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N GLU E 32 " pdb=" H1 GLU E 32 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C2 MAN M 5 " pdb=" O2 MAN M 5 " ideal model delta sigma weight residual 1.407 1.499 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C2 MAN Q 4 " pdb=" O2 MAN Q 4 " ideal model delta sigma weight residual 1.407 1.459 -0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 38814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 69458 3.93 - 7.86: 265 7.86 - 11.80: 33 11.80 - 15.73: 4 15.73 - 19.66: 9 Bond angle restraints: 69769 Sorted by residual: angle pdb=" C ALA F 512 " pdb=" N VAL F 513 " pdb=" CA VAL F 513 " ideal model delta sigma weight residual 121.70 141.36 -19.66 1.80e+00 3.09e-01 1.19e+02 angle pdb=" C ALA B 512 " pdb=" N VAL B 513 " pdb=" CA VAL B 513 " ideal model delta sigma weight residual 121.70 140.91 -19.21 1.80e+00 3.09e-01 1.14e+02 angle pdb=" C CYS A 54 " pdb=" N ALA A 55 " pdb=" CA ALA A 55 " ideal model delta sigma weight residual 121.70 140.77 -19.07 1.80e+00 3.09e-01 1.12e+02 angle pdb=" C CYS I 54 " pdb=" N ALA I 55 " pdb=" CA ALA I 55 " ideal model delta sigma weight residual 121.70 140.63 -18.93 1.80e+00 3.09e-01 1.11e+02 angle pdb=" C CYS E 54 " pdb=" N ALA E 55 " pdb=" CA ALA E 55 " ideal model delta sigma weight residual 121.70 140.47 -18.77 1.80e+00 3.09e-01 1.09e+02 ... (remaining 69764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 17516 22.75 - 45.51: 945 45.51 - 68.26: 268 68.26 - 91.01: 119 91.01 - 113.77: 24 Dihedral angle restraints: 18872 sinusoidal: 10497 harmonic: 8375 Sorted by residual: dihedral pdb=" CA LYS I 176 " pdb=" C LYS I 176 " pdb=" N PRO I 177 " pdb=" CA PRO I 177 " ideal model delta harmonic sigma weight residual -180.00 -140.90 -39.10 0 5.00e+00 4.00e-02 6.11e+01 dihedral pdb=" CA THR I 450 " pdb=" C THR I 450 " pdb=" N GLY I 451 " pdb=" CA GLY I 451 " ideal model delta harmonic sigma weight residual 180.00 141.48 38.52 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.42 -65.42 1 1.00e+01 1.00e-02 5.61e+01 ... (remaining 18869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.399: 3140 0.399 - 0.798: 0 0.798 - 1.197: 0 1.197 - 1.597: 0 1.597 - 1.996: 1 Chirality restraints: 3141 Sorted by residual: chirality pdb=" C5 MAN O 6 " pdb=" C4 MAN O 6 " pdb=" C6 MAN O 6 " pdb=" O5 MAN O 6 " both_signs ideal model delta sigma weight residual False -2.51 -0.51 -2.00 2.00e-01 2.50e+01 9.96e+01 chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 6.63e+00 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 3.01e+00 ... (remaining 3138 not shown) Planarity restraints: 5823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 176 " 0.119 5.00e-02 4.00e+02 1.79e-01 5.13e+01 pdb=" N PRO I 177 " -0.309 5.00e-02 4.00e+02 pdb=" CA PRO I 177 " 0.106 5.00e-02 4.00e+02 pdb=" CD PRO I 177 " 0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 176 " 0.119 5.00e-02 4.00e+02 1.78e-01 5.07e+01 pdb=" N PRO E 177 " -0.307 5.00e-02 4.00e+02 pdb=" CA PRO E 177 " 0.105 5.00e-02 4.00e+02 pdb=" CD PRO E 177 " 0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 176 " 0.118 5.00e-02 4.00e+02 1.76e-01 4.94e+01 pdb=" N PRO A 177 " -0.304 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " 0.102 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " 0.084 5.00e-02 4.00e+02 ... (remaining 5820 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 5436 2.27 - 2.85: 84490 2.85 - 3.43: 94638 3.43 - 4.02: 132663 4.02 - 4.60: 203034 Nonbonded interactions: 520261 Sorted by model distance: nonbonded pdb=" O MET I 369 " pdb=" HG1 THR I 373 " model vdw 1.686 2.450 nonbonded pdb=" O MET A 369 " pdb=" HG1 THR A 373 " model vdw 1.700 2.450 nonbonded pdb=" O MET E 369 " pdb=" HG1 THR E 373 " model vdw 1.705 2.450 nonbonded pdb=" O TRP K 101 " pdb=" HG SER K 108 " model vdw 1.705 2.450 nonbonded pdb=" H2 ALA J 512 " pdb=" O VAL J 513 " model vdw 1.705 2.450 ... (remaining 520256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 215 or (resid 216 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 217 through 505)) selection = chain 'E' selection = (chain 'I' and (resid 32 through 215 or (resid 216 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 217 through 505)) } 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 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } 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: 1.780 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: 0.270 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 40.270 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 0.092 20118 Z= 0.242 Angle : 0.992 19.660 27426 Z= 0.512 Chirality : 0.063 1.996 3141 Planarity : 0.007 0.179 3450 Dihedral : 15.322 113.768 7638 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.64 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.16), residues: 2454 helix: -0.75 (0.27), residues: 361 sheet: -0.96 (0.19), residues: 654 loop : -1.47 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 57 TYR 0.032 0.002 TYR D 48 PHE 0.017 0.002 PHE A 376 TRP 0.021 0.002 TRP A 112 HIS 0.025 0.002 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00550 (20052) covalent geometry : angle 0.96430 (27267) SS BOND : bond 0.00424 ( 39) SS BOND : angle 1.60232 ( 78) hydrogen bonds : bond 0.22613 ( 693) hydrogen bonds : angle 9.18334 ( 1863) link_ALPHA1-2 : bond 0.01464 ( 6) link_ALPHA1-2 : angle 5.32301 ( 18) link_ALPHA1-3 : bond 0.00366 ( 3) link_ALPHA1-3 : angle 3.02550 ( 9) link_BETA1-4 : bond 0.00962 ( 12) link_BETA1-4 : angle 4.43924 ( 36) link_NAG-ASN : bond 0.00703 ( 6) link_NAG-ASN : angle 2.44709 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8245 (tpp80) cc_final: 0.7947 (mmm-85) REVERT: D 52 GLU cc_start: 0.7266 (mm-30) cc_final: 0.7012 (tt0) REVERT: D 92 SER cc_start: 0.9143 (p) cc_final: 0.8654 (t) REVERT: E 104 MET cc_start: 0.8638 (ttt) cc_final: 0.8402 (ttt) REVERT: E 308 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7898 (mmm-85) REVERT: E 376 PHE cc_start: 0.8305 (m-80) cc_final: 0.7810 (m-10) REVERT: I 104 MET cc_start: 0.8661 (ttt) cc_final: 0.8405 (ttt) REVERT: I 304 ARG cc_start: 0.8597 (ttt180) cc_final: 0.8125 (ttt180) REVERT: L 52 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6816 (mt-10) REVERT: L 92 SER cc_start: 0.9140 (p) cc_final: 0.8791 (t) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.4355 time to fit residues: 233.6573 Evaluate side-chains 181 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS D 16 GLN E 114 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 651 ASN G 113 ASN I 355 ASN J 543 ASN J 651 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.135886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.115786 restraints weight = 94447.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115891 restraints weight = 115844.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117559 restraints weight = 89966.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117819 restraints weight = 65588.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.118214 restraints weight = 65966.743| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20118 Z= 0.169 Angle : 0.760 20.529 27426 Z= 0.388 Chirality : 0.047 0.267 3141 Planarity : 0.007 0.187 3450 Dihedral : 10.533 81.790 3207 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.48 % Favored : 92.95 % Rotamer: Outliers : 0.61 % Allowed : 6.53 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.17), residues: 2454 helix: -0.16 (0.28), residues: 359 sheet: -1.02 (0.19), residues: 720 loop : -1.33 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 500 TYR 0.020 0.002 TYR D 48 PHE 0.024 0.002 PHE A 376 TRP 0.023 0.001 TRP E 112 HIS 0.010 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00389 (20052) covalent geometry : angle 0.74563 (27267) SS BOND : bond 0.00761 ( 39) SS BOND : angle 1.13205 ( 78) hydrogen bonds : bond 0.05376 ( 693) hydrogen bonds : angle 6.54476 ( 1863) link_ALPHA1-2 : bond 0.00395 ( 6) link_ALPHA1-2 : angle 2.61220 ( 18) link_ALPHA1-3 : bond 0.00502 ( 3) link_ALPHA1-3 : angle 1.91702 ( 9) link_BETA1-4 : bond 0.00665 ( 12) link_BETA1-4 : angle 3.14617 ( 36) link_NAG-ASN : bond 0.00292 ( 6) link_NAG-ASN : angle 1.76675 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.986 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: C 122 LEU cc_start: 0.7729 (tp) cc_final: 0.7413 (tt) REVERT: D 92 SER cc_start: 0.9043 (p) cc_final: 0.8679 (t) REVERT: H 92 SER cc_start: 0.9282 (p) cc_final: 0.8867 (t) REVERT: L 92 SER cc_start: 0.9073 (p) cc_final: 0.8829 (t) outliers start: 13 outliers final: 10 residues processed: 205 average time/residue: 0.3558 time to fit residues: 109.8225 Evaluate side-chains 169 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain J residue 626 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 227 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 HIS F 543 ASN K 113 ASN K 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.115295 restraints weight = 95070.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.115396 restraints weight = 117554.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.117364 restraints weight = 91182.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.117450 restraints weight = 66538.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118345 restraints weight = 65378.675| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20118 Z= 0.164 Angle : 0.719 21.087 27426 Z= 0.364 Chirality : 0.046 0.225 3141 Planarity : 0.007 0.189 3450 Dihedral : 8.701 68.923 3207 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.13 % Favored : 92.38 % Rotamer: Outliers : 0.56 % Allowed : 8.34 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.17), residues: 2454 helix: 0.06 (0.28), residues: 358 sheet: -1.12 (0.19), residues: 747 loop : -1.44 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.020 0.002 TYR D 48 PHE 0.019 0.002 PHE I 376 TRP 0.019 0.001 TRP I 112 HIS 0.008 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00390 (20052) covalent geometry : angle 0.70645 (27267) SS BOND : bond 0.00337 ( 39) SS BOND : angle 1.17062 ( 78) hydrogen bonds : bond 0.04617 ( 693) hydrogen bonds : angle 6.05968 ( 1863) link_ALPHA1-2 : bond 0.00381 ( 6) link_ALPHA1-2 : angle 2.18959 ( 18) link_ALPHA1-3 : bond 0.00619 ( 3) link_ALPHA1-3 : angle 1.42217 ( 9) link_BETA1-4 : bond 0.00662 ( 12) link_BETA1-4 : angle 2.89451 ( 36) link_NAG-ASN : bond 0.00289 ( 6) link_NAG-ASN : angle 1.95829 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.875 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: C 122 LEU cc_start: 0.7756 (tp) cc_final: 0.7435 (tt) REVERT: D 92 SER cc_start: 0.9088 (p) cc_final: 0.8688 (t) REVERT: E 475 MET cc_start: 0.7343 (mtp) cc_final: 0.7137 (mtm) REVERT: H 92 SER cc_start: 0.9254 (p) cc_final: 0.8855 (t) REVERT: I 376 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: L 92 SER cc_start: 0.9072 (p) cc_final: 0.8826 (t) outliers start: 12 outliers final: 9 residues processed: 174 average time/residue: 0.2681 time to fit residues: 75.3983 Evaluate side-chains 162 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN C 116 HIS F 543 ASN G 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.132892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.115430 restraints weight = 95387.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115373 restraints weight = 129817.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.116539 restraints weight = 106484.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116752 restraints weight = 74562.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.117257 restraints weight = 67173.813| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20118 Z= 0.215 Angle : 0.737 22.514 27426 Z= 0.372 Chirality : 0.047 0.229 3141 Planarity : 0.007 0.194 3450 Dihedral : 7.848 58.107 3207 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.78 % Favored : 91.73 % Rotamer: Outliers : 1.21 % Allowed : 8.58 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.17), residues: 2454 helix: 0.23 (0.29), residues: 358 sheet: -1.22 (0.19), residues: 726 loop : -1.55 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 63 TYR 0.028 0.002 TYR D 48 PHE 0.027 0.002 PHE A 376 TRP 0.023 0.002 TRP A 112 HIS 0.011 0.002 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00521 (20052) covalent geometry : angle 0.72484 (27267) SS BOND : bond 0.00279 ( 39) SS BOND : angle 1.11433 ( 78) hydrogen bonds : bond 0.04119 ( 693) hydrogen bonds : angle 5.82670 ( 1863) link_ALPHA1-2 : bond 0.00246 ( 6) link_ALPHA1-2 : angle 2.01143 ( 18) link_ALPHA1-3 : bond 0.00524 ( 3) link_ALPHA1-3 : angle 1.37834 ( 9) link_BETA1-4 : bond 0.00684 ( 12) link_BETA1-4 : angle 2.84804 ( 36) link_NAG-ASN : bond 0.00415 ( 6) link_NAG-ASN : angle 2.07101 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.048 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: C 122 LEU cc_start: 0.7689 (tp) cc_final: 0.7365 (tt) REVERT: D 92 SER cc_start: 0.9085 (p) cc_final: 0.8703 (t) REVERT: E 308 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7932 (mmm-85) REVERT: E 376 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: E 475 MET cc_start: 0.7287 (mtp) cc_final: 0.7072 (mtm) REVERT: F 522 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7168 (t80) REVERT: L 92 SER cc_start: 0.9049 (p) cc_final: 0.8816 (t) outliers start: 26 outliers final: 20 residues processed: 174 average time/residue: 0.2939 time to fit residues: 80.9214 Evaluate side-chains 165 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 605 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.133661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.116748 restraints weight = 94746.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.116370 restraints weight = 120764.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.117148 restraints weight = 109393.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.117609 restraints weight = 80336.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117992 restraints weight = 77832.666| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 20118 Z= 0.152 Angle : 0.688 21.914 27426 Z= 0.347 Chirality : 0.045 0.228 3141 Planarity : 0.007 0.192 3450 Dihedral : 7.197 50.788 3207 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.93 % Favored : 92.58 % Rotamer: Outliers : 0.79 % Allowed : 9.51 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.17), residues: 2454 helix: 0.48 (0.29), residues: 358 sheet: -1.21 (0.19), residues: 753 loop : -1.58 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 585 TYR 0.024 0.001 TYR D 48 PHE 0.020 0.002 PHE A 376 TRP 0.018 0.001 TRP E 112 HIS 0.019 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00367 (20052) covalent geometry : angle 0.67781 (27267) SS BOND : bond 0.00300 ( 39) SS BOND : angle 1.13599 ( 78) hydrogen bonds : bond 0.03789 ( 693) hydrogen bonds : angle 5.59086 ( 1863) link_ALPHA1-2 : bond 0.00321 ( 6) link_ALPHA1-2 : angle 1.92607 ( 18) link_ALPHA1-3 : bond 0.00740 ( 3) link_ALPHA1-3 : angle 1.20945 ( 9) link_BETA1-4 : bond 0.00550 ( 12) link_BETA1-4 : angle 2.48228 ( 36) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 1.97793 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 LEU cc_start: 0.7649 (tp) cc_final: 0.7422 (tt) REVERT: D 92 SER cc_start: 0.9053 (p) cc_final: 0.8681 (t) REVERT: F 522 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6930 (t80) REVERT: L 92 SER cc_start: 0.9049 (p) cc_final: 0.8770 (t) outliers start: 17 outliers final: 14 residues processed: 167 average time/residue: 0.3020 time to fit residues: 81.2922 Evaluate side-chains 162 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 605 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 131 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 225 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN E 302 ASN F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.131809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114228 restraints weight = 95463.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113646 restraints weight = 122166.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.115156 restraints weight = 111019.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115144 restraints weight = 80863.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.115562 restraints weight = 80923.134| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20118 Z= 0.209 Angle : 0.721 22.606 27426 Z= 0.363 Chirality : 0.046 0.230 3141 Planarity : 0.007 0.194 3450 Dihedral : 7.324 53.727 3207 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.64 % Favored : 90.91 % Rotamer: Outliers : 1.31 % Allowed : 10.07 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.17), residues: 2454 helix: 0.45 (0.30), residues: 354 sheet: -1.30 (0.19), residues: 723 loop : -1.68 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 585 TYR 0.023 0.002 TYR D 48 PHE 0.028 0.002 PHE A 376 TRP 0.020 0.001 TRP E 112 HIS 0.017 0.002 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00508 (20052) covalent geometry : angle 0.70939 (27267) SS BOND : bond 0.00317 ( 39) SS BOND : angle 1.12469 ( 78) hydrogen bonds : bond 0.03858 ( 693) hydrogen bonds : angle 5.60013 ( 1863) link_ALPHA1-2 : bond 0.00227 ( 6) link_ALPHA1-2 : angle 1.92708 ( 18) link_ALPHA1-3 : bond 0.00614 ( 3) link_ALPHA1-3 : angle 1.30908 ( 9) link_BETA1-4 : bond 0.00649 ( 12) link_BETA1-4 : angle 2.70879 ( 36) link_NAG-ASN : bond 0.00428 ( 6) link_NAG-ASN : angle 2.11028 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.152 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 LEU cc_start: 0.7684 (tp) cc_final: 0.7460 (tt) REVERT: D 92 SER cc_start: 0.9086 (p) cc_final: 0.8713 (t) REVERT: E 376 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: F 522 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7333 (t80) REVERT: I 376 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7774 (m-10) REVERT: L 92 SER cc_start: 0.9091 (p) cc_final: 0.8812 (t) outliers start: 28 outliers final: 21 residues processed: 171 average time/residue: 0.3170 time to fit residues: 86.6327 Evaluate side-chains 167 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 605 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 78 optimal weight: 10.0000 chunk 238 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.134430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.117803 restraints weight = 94646.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.117470 restraints weight = 118650.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.118408 restraints weight = 93294.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.118482 restraints weight = 70498.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.118789 restraints weight = 64109.357| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20118 Z= 0.113 Angle : 0.656 21.262 27426 Z= 0.330 Chirality : 0.044 0.231 3141 Planarity : 0.007 0.190 3450 Dihedral : 6.378 45.813 3207 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.15 % Favored : 93.44 % Rotamer: Outliers : 1.12 % Allowed : 10.86 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.17), residues: 2454 helix: 0.79 (0.30), residues: 354 sheet: -1.22 (0.19), residues: 750 loop : -1.58 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 308 TYR 0.023 0.001 TYR D 48 PHE 0.031 0.002 PHE A 376 TRP 0.016 0.001 TRP E 112 HIS 0.015 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (20052) covalent geometry : angle 0.64687 (27267) SS BOND : bond 0.00253 ( 39) SS BOND : angle 1.02850 ( 78) hydrogen bonds : bond 0.03433 ( 693) hydrogen bonds : angle 5.30043 ( 1863) link_ALPHA1-2 : bond 0.00402 ( 6) link_ALPHA1-2 : angle 1.88044 ( 18) link_ALPHA1-3 : bond 0.00874 ( 3) link_ALPHA1-3 : angle 1.14840 ( 9) link_BETA1-4 : bond 0.00539 ( 12) link_BETA1-4 : angle 2.15195 ( 36) link_NAG-ASN : bond 0.00229 ( 6) link_NAG-ASN : angle 1.89410 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.127 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: C 122 LEU cc_start: 0.7618 (tp) cc_final: 0.7373 (tt) REVERT: D 92 SER cc_start: 0.9053 (p) cc_final: 0.8658 (t) REVERT: F 522 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6815 (t80) REVERT: H 92 SER cc_start: 0.9148 (p) cc_final: 0.8750 (t) REVERT: L 92 SER cc_start: 0.9046 (p) cc_final: 0.8737 (t) outliers start: 24 outliers final: 21 residues processed: 171 average time/residue: 0.3140 time to fit residues: 85.4113 Evaluate side-chains 167 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 605 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 56 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113822 restraints weight = 95897.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112753 restraints weight = 126053.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114431 restraints weight = 105747.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114597 restraints weight = 79228.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.115312 restraints weight = 80428.093| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20118 Z= 0.218 Angle : 0.715 22.286 27426 Z= 0.360 Chirality : 0.046 0.232 3141 Planarity : 0.007 0.193 3450 Dihedral : 6.640 59.965 3207 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.56 % Favored : 91.08 % Rotamer: Outliers : 1.21 % Allowed : 11.52 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.17), residues: 2454 helix: 0.63 (0.30), residues: 354 sheet: -1.29 (0.19), residues: 729 loop : -1.69 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 585 TYR 0.024 0.002 TYR D 48 PHE 0.025 0.002 PHE J 522 TRP 0.019 0.002 TRP E 112 HIS 0.014 0.002 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00527 (20052) covalent geometry : angle 0.70380 (27267) SS BOND : bond 0.00274 ( 39) SS BOND : angle 1.16239 ( 78) hydrogen bonds : bond 0.03713 ( 693) hydrogen bonds : angle 5.42903 ( 1863) link_ALPHA1-2 : bond 0.00249 ( 6) link_ALPHA1-2 : angle 1.86044 ( 18) link_ALPHA1-3 : bond 0.00562 ( 3) link_ALPHA1-3 : angle 1.39369 ( 9) link_BETA1-4 : bond 0.00672 ( 12) link_BETA1-4 : angle 2.65278 ( 36) link_NAG-ASN : bond 0.00501 ( 6) link_NAG-ASN : angle 2.13377 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 LEU cc_start: 0.7691 (tp) cc_final: 0.7475 (tt) REVERT: D 92 SER cc_start: 0.9092 (p) cc_final: 0.8715 (t) REVERT: F 522 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7277 (t80) REVERT: I 376 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: L 92 SER cc_start: 0.9087 (p) cc_final: 0.8806 (t) outliers start: 26 outliers final: 23 residues processed: 163 average time/residue: 0.3083 time to fit residues: 81.5815 Evaluate side-chains 164 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 605 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 221 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 227 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.132287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114653 restraints weight = 95313.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114596 restraints weight = 141654.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115618 restraints weight = 108293.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116203 restraints weight = 80349.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.116299 restraints weight = 78575.940| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20118 Z= 0.164 Angle : 0.686 22.159 27426 Z= 0.345 Chirality : 0.045 0.233 3141 Planarity : 0.007 0.193 3450 Dihedral : 6.248 36.450 3207 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.46 % Favored : 92.18 % Rotamer: Outliers : 1.21 % Allowed : 11.47 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.17), residues: 2454 helix: 0.71 (0.30), residues: 354 sheet: -1.26 (0.19), residues: 753 loop : -1.75 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 308 TYR 0.024 0.001 TYR D 48 PHE 0.017 0.002 PHE I 376 TRP 0.016 0.001 TRP E 112 HIS 0.015 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00400 (20052) covalent geometry : angle 0.67597 (27267) SS BOND : bond 0.00289 ( 39) SS BOND : angle 1.08884 ( 78) hydrogen bonds : bond 0.03537 ( 693) hydrogen bonds : angle 5.32480 ( 1863) link_ALPHA1-2 : bond 0.00352 ( 6) link_ALPHA1-2 : angle 1.86182 ( 18) link_ALPHA1-3 : bond 0.00671 ( 3) link_ALPHA1-3 : angle 1.23576 ( 9) link_BETA1-4 : bond 0.00597 ( 12) link_BETA1-4 : angle 2.36074 ( 36) link_NAG-ASN : bond 0.00307 ( 6) link_NAG-ASN : angle 1.97868 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.052 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: C 122 LEU cc_start: 0.7634 (tp) cc_final: 0.7406 (tt) REVERT: D 92 SER cc_start: 0.9068 (p) cc_final: 0.8693 (t) REVERT: E 376 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7520 (m-10) REVERT: F 522 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7079 (t80) REVERT: I 376 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: L 92 SER cc_start: 0.9083 (p) cc_final: 0.8788 (t) outliers start: 26 outliers final: 21 residues processed: 163 average time/residue: 0.2748 time to fit residues: 73.0638 Evaluate side-chains 167 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 605 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 99 optimal weight: 0.9990 chunk 36 optimal weight: 0.0470 chunk 90 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.134401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.117188 restraints weight = 94964.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117243 restraints weight = 124915.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.118565 restraints weight = 95540.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.118659 restraints weight = 73188.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.119015 restraints weight = 66299.544| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 20118 Z= 0.112 Angle : 0.640 20.872 27426 Z= 0.323 Chirality : 0.044 0.235 3141 Planarity : 0.007 0.189 3450 Dihedral : 5.672 39.690 3207 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.89 % Favored : 92.75 % Rotamer: Outliers : 0.93 % Allowed : 11.89 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.17), residues: 2454 helix: 0.80 (0.29), residues: 370 sheet: -1.10 (0.19), residues: 801 loop : -1.63 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 308 TYR 0.020 0.001 TYR L 51 PHE 0.018 0.001 PHE B 519 TRP 0.015 0.001 TRP E 112 HIS 0.013 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00273 (20052) covalent geometry : angle 0.63170 (27267) SS BOND : bond 0.00252 ( 39) SS BOND : angle 1.01244 ( 78) hydrogen bonds : bond 0.03191 ( 693) hydrogen bonds : angle 5.07414 ( 1863) link_ALPHA1-2 : bond 0.00416 ( 6) link_ALPHA1-2 : angle 1.83212 ( 18) link_ALPHA1-3 : bond 0.00722 ( 3) link_ALPHA1-3 : angle 1.22992 ( 9) link_BETA1-4 : bond 0.00524 ( 12) link_BETA1-4 : angle 1.96969 ( 36) link_NAG-ASN : bond 0.00216 ( 6) link_NAG-ASN : angle 1.84169 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.138 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: C 43 GLN cc_start: 0.7323 (mp10) cc_final: 0.6943 (mp10) REVERT: C 122 LEU cc_start: 0.7587 (tp) cc_final: 0.7356 (tt) REVERT: D 92 SER cc_start: 0.9018 (p) cc_final: 0.8662 (t) REVERT: F 522 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6850 (t80) REVERT: H 92 SER cc_start: 0.9122 (p) cc_final: 0.8745 (t) REVERT: L 92 SER cc_start: 0.9045 (p) cc_final: 0.8756 (t) outliers start: 20 outliers final: 18 residues processed: 173 average time/residue: 0.3020 time to fit residues: 84.6690 Evaluate side-chains 167 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain J residue 605 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 203 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 186 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.133808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115151 restraints weight = 94961.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114724 restraints weight = 138412.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.116270 restraints weight = 105861.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.116793 restraints weight = 81359.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.116985 restraints weight = 78400.562| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20118 Z= 0.132 Angle : 0.644 20.745 27426 Z= 0.325 Chirality : 0.044 0.231 3141 Planarity : 0.007 0.188 3450 Dihedral : 5.650 39.851 3207 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.89 % Favored : 92.75 % Rotamer: Outliers : 1.12 % Allowed : 11.89 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.17), residues: 2454 helix: 1.05 (0.30), residues: 354 sheet: -1.11 (0.19), residues: 801 loop : -1.61 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 308 TYR 0.020 0.001 TYR D 48 PHE 0.018 0.002 PHE I 376 TRP 0.015 0.001 TRP E 112 HIS 0.013 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00324 (20052) covalent geometry : angle 0.63509 (27267) SS BOND : bond 0.00250 ( 39) SS BOND : angle 1.01646 ( 78) hydrogen bonds : bond 0.03217 ( 693) hydrogen bonds : angle 5.05492 ( 1863) link_ALPHA1-2 : bond 0.00379 ( 6) link_ALPHA1-2 : angle 1.83217 ( 18) link_ALPHA1-3 : bond 0.00659 ( 3) link_ALPHA1-3 : angle 1.27943 ( 9) link_BETA1-4 : bond 0.00544 ( 12) link_BETA1-4 : angle 2.05760 ( 36) link_NAG-ASN : bond 0.00298 ( 6) link_NAG-ASN : angle 1.87894 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4966.99 seconds wall clock time: 85 minutes 59.37 seconds (5159.37 seconds total)