Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 12:48:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/04_2023/7nku_12448_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/04_2023/7nku_12448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/04_2023/7nku_12448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/04_2023/7nku_12448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/04_2023/7nku_12448_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/04_2023/7nku_12448_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.039 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 120 5.16 5 B 6 2.79 5 C 15834 2.51 5 N 4344 2.21 5 O 4992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 676": "OD1" <-> "OD2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 456": "OD1" <-> "OD2" Residue "B ASP 517": "OD1" <-> "OD2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 708": "OD1" <-> "OD2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 345": "OD1" <-> "OD2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C GLU 522": "OE1" <-> "OE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 708": "OD1" <-> "OD2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ASP 396": "OD1" <-> "OD2" Residue "D PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 421": "OD1" <-> "OD2" Residue "D ASP 433": "OD1" <-> "OD2" Residue "D ASP 456": "OD1" <-> "OD2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ASP 421": "OD1" <-> "OD2" Residue "E ASP 433": "OD1" <-> "OD2" Residue "E GLU 522": "OE1" <-> "OE2" Residue "E TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 708": "OD1" <-> "OD2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F ASP 421": "OD1" <-> "OD2" Residue "F ASP 433": "OD1" <-> "OD2" Residue "F ASP 517": "OD1" <-> "OD2" Residue "F ASP 663": "OD1" <-> "OD2" Residue "F PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 708": "OD1" <-> "OD2" Residue "F GLU 738": "OE1" <-> "OE2" Residue "F ASP 741": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 25332 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "B" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "C" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "D" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "E" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "F" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'AGS': 2, 'TDB': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'AGS': 2, 'TDB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'AGS': 2, 'TDB': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'AGS': 2, 'TDB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.43, per 1000 atoms: 0.53 Number of scatterers: 25332 At special positions: 0 Unit cell: (138.86, 136.74, 98.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 36 15.00 O 4992 8.00 N 4344 7.00 C 15834 6.00 B 6 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.71 Conformation dependent library (CDL) restraints added in 3.6 seconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 12 sheets defined 48.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.854A pdb=" N ALA A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 416 through 429 Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 454 through 475 removed outlier: 4.017A pdb=" N THR A 475 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 498 removed outlier: 4.174A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 537 Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 584 through 587 No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 593 through 607 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 627 through 644 removed outlier: 5.147A pdb=" N ALA A 633 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASN A 634 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 709 through 715 Processing helix chain 'A' and resid 721 through 738 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.632A pdb=" N ARG A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 266 Proline residue: B 264 - end of helix Processing helix chain 'B' and resid 269 through 272 No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 320 through 336 removed outlier: 3.779A pdb=" N ALA B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 416 through 429 Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'B' and resid 454 through 475 removed outlier: 4.205A pdb=" N THR B 475 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 498 removed outlier: 4.420A pdb=" N ASP B 497 " --> pdb=" O SER B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 537 Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'B' and resid 564 through 574 Processing helix chain 'B' and resid 584 through 587 No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 591 through 607 removed outlier: 3.554A pdb=" N GLU B 595 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 627 through 644 removed outlier: 5.421A pdb=" N ALA B 633 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 709 through 715 Processing helix chain 'B' and resid 721 through 738 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'C' and resid 251 through 263 Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 320 through 336 removed outlier: 4.125A pdb=" N ALA C 325 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 363 through 374 Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 439 through 447 Processing helix chain 'C' and resid 454 through 475 removed outlier: 4.067A pdb=" N THR C 475 " --> pdb=" O GLY C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 498 removed outlier: 4.218A pdb=" N ASP C 497 " --> pdb=" O SER C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 537 Proline residue: C 535 - end of helix Processing helix chain 'C' and resid 539 through 545 Processing helix chain 'C' and resid 564 through 572 Processing helix chain 'C' and resid 583 through 585 No H-bonds generated for 'chain 'C' and resid 583 through 585' Processing helix chain 'C' and resid 591 through 607 removed outlier: 4.022A pdb=" N GLU C 595 " --> pdb=" O VAL C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 627 through 644 removed outlier: 5.505A pdb=" N ALA C 633 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN C 634 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 667 through 669 No H-bonds generated for 'chain 'C' and resid 667 through 669' Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'C' and resid 721 through 738 Processing helix chain 'C' and resid 747 through 756 Processing helix chain 'C' and resid 763 through 774 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 292 through 302 Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 320 through 336 removed outlier: 4.064A pdb=" N ALA D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 363 through 374 Processing helix chain 'D' and resid 397 through 400 No H-bonds generated for 'chain 'D' and resid 397 through 400' Processing helix chain 'D' and resid 416 through 429 Processing helix chain 'D' and resid 439 through 447 Processing helix chain 'D' and resid 454 through 475 removed outlier: 4.510A pdb=" N THR D 475 " --> pdb=" O GLY D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 498 removed outlier: 4.300A pdb=" N ASP D 497 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 537 Proline residue: D 535 - end of helix Processing helix chain 'D' and resid 539 through 545 Processing helix chain 'D' and resid 564 through 572 Processing helix chain 'D' and resid 583 through 586 No H-bonds generated for 'chain 'D' and resid 583 through 586' Processing helix chain 'D' and resid 591 through 607 removed outlier: 4.450A pdb=" N ALA D 597 " --> pdb=" O GLU D 593 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE D 598 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 620 No H-bonds generated for 'chain 'D' and resid 618 through 620' Processing helix chain 'D' and resid 629 through 645 removed outlier: 5.246A pdb=" N ASN D 634 " --> pdb=" O THR D 630 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N HIS D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 667 through 669 No H-bonds generated for 'chain 'D' and resid 667 through 669' Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 709 through 715 Processing helix chain 'D' and resid 721 through 738 Processing helix chain 'D' and resid 747 through 756 Processing helix chain 'D' and resid 763 through 774 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 268 through 273 Processing helix chain 'E' and resid 292 through 302 Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 320 through 336 removed outlier: 3.939A pdb=" N ALA E 325 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 363 through 374 Processing helix chain 'E' and resid 397 through 400 No H-bonds generated for 'chain 'E' and resid 397 through 400' Processing helix chain 'E' and resid 416 through 429 Processing helix chain 'E' and resid 439 through 447 Processing helix chain 'E' and resid 454 through 475 removed outlier: 4.352A pdb=" N THR E 475 " --> pdb=" O GLY E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 498 removed outlier: 4.131A pdb=" N ASP E 497 " --> pdb=" O SER E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 537 Proline residue: E 535 - end of helix Processing helix chain 'E' and resid 539 through 545 Processing helix chain 'E' and resid 564 through 574 Processing helix chain 'E' and resid 583 through 586 No H-bonds generated for 'chain 'E' and resid 583 through 586' Processing helix chain 'E' and resid 591 through 607 Processing helix chain 'E' and resid 618 through 620 No H-bonds generated for 'chain 'E' and resid 618 through 620' Processing helix chain 'E' and resid 627 through 645 removed outlier: 3.685A pdb=" N SER E 631 " --> pdb=" O SER E 628 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA E 633 " --> pdb=" O THR E 630 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ASN E 634 " --> pdb=" O SER E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 667 through 669 No H-bonds generated for 'chain 'E' and resid 667 through 669' Processing helix chain 'E' and resid 686 through 696 Processing helix chain 'E' and resid 709 through 715 Processing helix chain 'E' and resid 721 through 738 Processing helix chain 'E' and resid 747 through 755 Processing helix chain 'E' and resid 763 through 775 Processing helix chain 'F' and resid 251 through 263 Processing helix chain 'F' and resid 269 through 272 No H-bonds generated for 'chain 'F' and resid 269 through 272' Processing helix chain 'F' and resid 292 through 302 Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 320 through 336 removed outlier: 4.116A pdb=" N ALA F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 363 through 374 Processing helix chain 'F' and resid 397 through 400 No H-bonds generated for 'chain 'F' and resid 397 through 400' Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'F' and resid 439 through 447 Processing helix chain 'F' and resid 454 through 475 removed outlier: 4.381A pdb=" N THR F 475 " --> pdb=" O GLY F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 498 Processing helix chain 'F' and resid 522 through 531 Processing helix chain 'F' and resid 539 through 545 Processing helix chain 'F' and resid 564 through 574 Processing helix chain 'F' and resid 583 through 586 No H-bonds generated for 'chain 'F' and resid 583 through 586' Processing helix chain 'F' and resid 591 through 607 Processing helix chain 'F' and resid 618 through 620 No H-bonds generated for 'chain 'F' and resid 618 through 620' Processing helix chain 'F' and resid 627 through 645 removed outlier: 5.121A pdb=" N ASN F 634 " --> pdb=" O THR F 630 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS F 635 " --> pdb=" O SER F 631 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 636 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'F' and resid 686 through 696 Processing helix chain 'F' and resid 703 through 705 No H-bonds generated for 'chain 'F' and resid 703 through 705' Processing helix chain 'F' and resid 709 through 715 Processing helix chain 'F' and resid 721 through 738 Processing helix chain 'F' and resid 747 through 756 Processing helix chain 'F' and resid 763 through 775 Processing sheet with id= A, first strand: chain 'A' and resid 407 through 409 removed outlier: 6.640A pdb=" N SER A 340 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE A 386 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 342 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA A 388 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 344 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS A 306 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE A 343 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 308 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASP A 345 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 310 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 677 through 680 removed outlier: 8.594A pdb=" N VAL A 553 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 655 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 555 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A 657 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 611 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL A 656 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE A 613 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA A 658 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 615 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A 577 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE A 614 " --> pdb=" O ASN A 577 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 579 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP A 616 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 581 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 407 through 409 removed outlier: 6.588A pdb=" N SER B 340 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 386 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE B 342 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA B 388 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 344 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS B 306 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 343 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 308 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP B 345 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE B 310 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 580 through 582 removed outlier: 7.535A pdb=" N VAL B 581 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE B 614 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 554 " --> pdb=" O ASP B 676 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS B 678 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR B 556 " --> pdb=" O HIS B 678 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B 680 " --> pdb=" O TYR B 556 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 306 through 310 removed outlier: 4.487A pdb=" N ASP C 345 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU C 283 " --> pdb=" O ASP C 406 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU C 408 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 577 through 582 removed outlier: 6.176A pdb=" N LEU C 554 " --> pdb=" O ASP C 676 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS C 678 " --> pdb=" O LEU C 554 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR C 556 " --> pdb=" O HIS C 678 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C 680 " --> pdb=" O TYR C 556 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 407 through 409 removed outlier: 6.445A pdb=" N SER D 340 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE D 386 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE D 342 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA D 388 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE D 344 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS D 306 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE D 343 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU D 308 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASP D 345 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE D 310 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 677 through 680 removed outlier: 8.602A pdb=" N VAL D 553 " --> pdb=" O VAL D 653 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE D 655 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU D 555 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 657 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER D 611 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 656 " --> pdb=" O SER D 611 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 613 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA D 658 " --> pdb=" O ILE D 613 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE D 615 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN D 577 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE D 614 " --> pdb=" O ASN D 577 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU D 579 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP D 616 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 581 " --> pdb=" O ASP D 616 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 407 through 409 removed outlier: 6.518A pdb=" N SER E 340 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE E 386 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE E 342 " --> pdb=" O ILE E 386 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ALA E 388 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE E 344 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS E 306 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE E 343 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU E 308 " --> pdb=" O PHE E 343 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP E 345 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE E 310 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 677 through 680 removed outlier: 8.805A pdb=" N VAL E 553 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE E 655 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU E 555 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA E 657 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER E 611 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL E 656 " --> pdb=" O SER E 611 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE E 613 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA E 658 " --> pdb=" O ILE E 613 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE E 615 " --> pdb=" O ALA E 658 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP E 616 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 407 through 410 removed outlier: 6.412A pdb=" N SER F 340 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE F 386 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE F 342 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA F 388 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE F 344 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS F 306 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE F 343 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU F 308 " --> pdb=" O PHE F 343 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP F 345 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE F 310 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 677 through 680 removed outlier: 8.762A pdb=" N VAL F 553 " --> pdb=" O VAL F 653 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 655 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU F 555 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA F 657 " --> pdb=" O LEU F 555 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER F 611 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL F 656 " --> pdb=" O SER F 611 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE F 613 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA F 658 " --> pdb=" O ILE F 613 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE F 615 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN F 577 " --> pdb=" O ILE F 612 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE F 614 " --> pdb=" O ASN F 577 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU F 579 " --> pdb=" O PHE F 614 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP F 616 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 581 " --> pdb=" O ASP F 616 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2538 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: 8.45 Time building geometry restraints manager: 11.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 8727 1.37 - 1.51: 7864 1.51 - 1.66: 8987 1.66 - 1.80: 163 1.80 - 1.95: 41 Bond restraints: 25782 Sorted by residual: bond pdb=" C14 TDB A 903 " pdb=" S1 TDB A 903 " ideal model delta sigma weight residual 1.717 1.868 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C14 TDB F 801 " pdb=" S1 TDB F 801 " ideal model delta sigma weight residual 1.717 1.868 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C14 TDB D 801 " pdb=" S1 TDB D 801 " ideal model delta sigma weight residual 1.717 1.867 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C14 TDB C 801 " pdb=" S1 TDB C 801 " ideal model delta sigma weight residual 1.717 1.867 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C14 TDB D 804 " pdb=" S1 TDB D 804 " ideal model delta sigma weight residual 1.717 1.866 -0.149 2.00e-02 2.50e+03 5.53e+01 ... (remaining 25777 not shown) Histogram of bond angle deviations from ideal: 88.75 - 97.84: 7 97.84 - 106.93: 974 106.93 - 116.02: 16327 116.02 - 125.11: 17317 125.11 - 134.20: 361 Bond angle restraints: 34986 Sorted by residual: angle pdb=" C13 TDB D 804 " pdb=" B1 TDB D 804 " pdb=" O1 TDB D 804 " ideal model delta sigma weight residual 127.55 104.96 22.59 3.00e+00 1.11e-01 5.67e+01 angle pdb=" C13 TDB A 904 " pdb=" B1 TDB A 904 " pdb=" O1 TDB A 904 " ideal model delta sigma weight residual 127.55 105.30 22.25 3.00e+00 1.11e-01 5.50e+01 angle pdb=" O15 TDB D 801 " pdb=" S15 TDB D 801 " pdb=" O16 TDB D 801 " ideal model delta sigma weight residual 118.86 102.15 16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C13 TDB F 801 " pdb=" B1 TDB F 801 " pdb=" O1 TDB F 801 " ideal model delta sigma weight residual 127.55 110.88 16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O15 TDB C 801 " pdb=" S15 TDB C 801 " pdb=" O16 TDB C 801 " ideal model delta sigma weight residual 118.86 102.27 16.59 3.00e+00 1.11e-01 3.06e+01 ... (remaining 34981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 15387 33.37 - 66.74: 341 66.74 - 100.11: 23 100.11 - 133.48: 1 133.48 - 166.85: 10 Dihedral angle restraints: 15762 sinusoidal: 6420 harmonic: 9342 Sorted by residual: dihedral pdb=" CA ASN A 588 " pdb=" C ASN A 588 " pdb=" N LYS A 589 " pdb=" CA LYS A 589 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA GLU D 573 " pdb=" C GLU D 573 " pdb=" N SER D 574 " pdb=" CA SER D 574 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLU A 573 " pdb=" C GLU A 573 " pdb=" N SER A 574 " pdb=" CA SER A 574 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 15759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3094 0.058 - 0.115: 803 0.115 - 0.173: 114 0.173 - 0.231: 5 0.231 - 0.288: 4 Chirality restraints: 4020 Sorted by residual: chirality pdb=" CB ILE A 498 " pdb=" CA ILE A 498 " pdb=" CG1 ILE A 498 " pdb=" CG2 ILE A 498 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU B 457 " pdb=" CB LEU B 457 " pdb=" CD1 LEU B 457 " pdb=" CD2 LEU B 457 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU F 457 " pdb=" CB LEU F 457 " pdb=" CD1 LEU F 457 " pdb=" CD2 LEU F 457 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4017 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" B1 TDB D 804 " -0.269 2.00e-02 2.50e+03 2.93e-01 2.57e+03 pdb=" C12 TDB D 804 " -0.195 2.00e-02 2.50e+03 pdb=" C13 TDB D 804 " -0.145 2.00e-02 2.50e+03 pdb=" C14 TDB D 804 " 0.061 2.00e-02 2.50e+03 pdb=" C2 TDB D 804 " 0.150 2.00e-02 2.50e+03 pdb=" C7 TDB D 804 " -0.063 2.00e-02 2.50e+03 pdb=" C8 TDB D 804 " -0.106 2.00e-02 2.50e+03 pdb=" N1 TDB D 804 " -0.190 2.00e-02 2.50e+03 pdb=" N2 TDB D 804 " 0.033 2.00e-02 2.50e+03 pdb=" O1 TDB D 804 " 0.841 2.00e-02 2.50e+03 pdb=" S1 TDB D 804 " 0.169 2.00e-02 2.50e+03 pdb=" S15 TDB D 804 " -0.286 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B1 TDB A 904 " 0.265 2.00e-02 2.50e+03 2.92e-01 2.55e+03 pdb=" C12 TDB A 904 " 0.191 2.00e-02 2.50e+03 pdb=" C13 TDB A 904 " 0.140 2.00e-02 2.50e+03 pdb=" C14 TDB A 904 " -0.061 2.00e-02 2.50e+03 pdb=" C2 TDB A 904 " -0.147 2.00e-02 2.50e+03 pdb=" C7 TDB A 904 " 0.066 2.00e-02 2.50e+03 pdb=" C8 TDB A 904 " 0.107 2.00e-02 2.50e+03 pdb=" N1 TDB A 904 " 0.189 2.00e-02 2.50e+03 pdb=" N2 TDB A 904 " -0.032 2.00e-02 2.50e+03 pdb=" O1 TDB A 904 " -0.839 2.00e-02 2.50e+03 pdb=" S1 TDB A 904 " -0.168 2.00e-02 2.50e+03 pdb=" S15 TDB A 904 " 0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B1 TDB D 801 " -0.246 2.00e-02 2.50e+03 2.48e-01 1.84e+03 pdb=" C12 TDB D 801 " -0.173 2.00e-02 2.50e+03 pdb=" C13 TDB D 801 " -0.120 2.00e-02 2.50e+03 pdb=" C14 TDB D 801 " 0.058 2.00e-02 2.50e+03 pdb=" C2 TDB D 801 " 0.144 2.00e-02 2.50e+03 pdb=" C7 TDB D 801 " -0.057 2.00e-02 2.50e+03 pdb=" C8 TDB D 801 " -0.096 2.00e-02 2.50e+03 pdb=" N1 TDB D 801 " -0.147 2.00e-02 2.50e+03 pdb=" N2 TDB D 801 " 0.039 2.00e-02 2.50e+03 pdb=" O1 TDB D 801 " 0.694 2.00e-02 2.50e+03 pdb=" S1 TDB D 801 " 0.158 2.00e-02 2.50e+03 pdb=" S15 TDB D 801 " -0.255 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 324 2.57 - 3.15: 23516 3.15 - 3.73: 40853 3.73 - 4.32: 54964 4.32 - 4.90: 86253 Nonbonded interactions: 205910 Sorted by model distance: nonbonded pdb=" OG SER A 720 " pdb=" OE1 GLU A 723 " model vdw 1.986 2.440 nonbonded pdb=" OG SER D 720 " pdb=" OE1 GLU D 723 " model vdw 1.992 2.440 nonbonded pdb=" O2B AGS E 901 " pdb=" O2G AGS E 901 " model vdw 1.998 2.440 nonbonded pdb=" O2B AGS A 901 " pdb=" O3G AGS A 901 " model vdw 2.007 2.440 nonbonded pdb=" O2B AGS D 802 " pdb=" O2G AGS D 802 " model vdw 2.020 2.440 ... (remaining 205905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 239 through 780 or resid 902)) selection = (chain 'B' and (resid 239 through 780 or resid 902)) selection = (chain 'C' and (resid 239 through 780 or resid 802)) selection = (chain 'D' and (resid 239 through 780 or resid 802)) selection = (chain 'E' and (resid 239 through 780 or resid 902)) selection = (chain 'F' and (resid 239 through 780 or resid 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.890 Check model and map are aligned: 0.400 Set scattering table: 0.220 Process input model: 63.740 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.008 0.151 25782 Z= 0.488 Angle : 0.941 22.586 34986 Z= 0.469 Chirality : 0.052 0.288 4020 Planarity : 0.011 0.293 4488 Dihedral : 14.980 166.853 9738 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3240 helix: 0.00 (0.13), residues: 1548 sheet: -0.10 (0.28), residues: 402 loop : -0.90 (0.18), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1040 time to evaluate : 2.895 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 outliers start: 0 outliers final: 0 residues processed: 1040 average time/residue: 0.4604 time to fit residues: 691.8239 Evaluate side-chains 926 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 926 time to evaluate : 2.617 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 GLN C 407 GLN D 267 GLN ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN E 729 GLN F 301 ASN F 729 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 25782 Z= 0.246 Angle : 0.728 11.799 34986 Z= 0.366 Chirality : 0.046 0.228 4020 Planarity : 0.006 0.104 4488 Dihedral : 12.413 167.561 3684 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3240 helix: 0.04 (0.13), residues: 1578 sheet: 0.24 (0.29), residues: 354 loop : -0.65 (0.18), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 959 time to evaluate : 2.625 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 outliers start: 53 outliers final: 26 residues processed: 970 average time/residue: 0.4665 time to fit residues: 648.3354 Evaluate side-chains 907 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 881 time to evaluate : 2.857 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2690 time to fit residues: 16.0930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 200 optimal weight: 0.0970 chunk 81 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 0.0470 chunk 292 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS C 393 ASN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 ASN ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN D 407 GLN F 701 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25782 Z= 0.208 Angle : 0.687 11.425 34986 Z= 0.344 Chirality : 0.044 0.223 4020 Planarity : 0.006 0.076 4488 Dihedral : 12.161 176.212 3684 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3240 helix: 0.04 (0.13), residues: 1602 sheet: 0.29 (0.29), residues: 366 loop : -0.50 (0.19), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 903 time to evaluate : 2.981 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 outliers start: 36 outliers final: 19 residues processed: 918 average time/residue: 0.4919 time to fit residues: 652.8173 Evaluate side-chains 866 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 847 time to evaluate : 2.832 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2738 time to fit residues: 13.0998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 313 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 ASN B 311 ASN C 407 GLN C 521 GLN C 687 ASN D 393 ASN D 426 GLN E 729 GLN ** F 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 25782 Z= 0.208 Angle : 0.667 11.344 34986 Z= 0.334 Chirality : 0.043 0.208 4020 Planarity : 0.005 0.087 4488 Dihedral : 11.994 178.918 3684 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3240 helix: 0.22 (0.13), residues: 1572 sheet: 0.23 (0.29), residues: 384 loop : -0.51 (0.19), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 868 time to evaluate : 2.988 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 outliers start: 60 outliers final: 31 residues processed: 883 average time/residue: 0.4781 time to fit residues: 607.8152 Evaluate side-chains 856 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 825 time to evaluate : 2.726 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2516 time to fit residues: 18.0498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 3.9990 chunk 177 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 311 ASN C 687 ASN F 393 ASN F 426 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 25782 Z= 0.219 Angle : 0.677 12.736 34986 Z= 0.336 Chirality : 0.044 0.244 4020 Planarity : 0.005 0.082 4488 Dihedral : 11.857 174.565 3684 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3240 helix: 0.27 (0.13), residues: 1566 sheet: 0.44 (0.29), residues: 366 loop : -0.46 (0.19), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 866 time to evaluate : 3.121 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 outliers start: 49 outliers final: 19 residues processed: 890 average time/residue: 0.4760 time to fit residues: 610.5258 Evaluate side-chains 846 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 827 time to evaluate : 3.411 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2903 time to fit residues: 13.4640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.5980 chunk 282 optimal weight: 0.0170 chunk 61 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 313 optimal weight: 0.0770 chunk 260 optimal weight: 0.2980 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN E 301 ASN F 426 GLN F 729 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 25782 Z= 0.193 Angle : 0.694 15.707 34986 Z= 0.341 Chirality : 0.044 0.333 4020 Planarity : 0.005 0.082 4488 Dihedral : 11.727 171.357 3684 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3240 helix: 0.29 (0.13), residues: 1554 sheet: 0.39 (0.29), residues: 378 loop : -0.44 (0.19), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 832 time to evaluate : 3.030 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 outliers start: 60 outliers final: 28 residues processed: 856 average time/residue: 0.4780 time to fit residues: 590.2497 Evaluate side-chains 831 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 803 time to evaluate : 2.995 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2306 time to fit residues: 16.2421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 178 optimal weight: 0.0670 chunk 228 optimal weight: 0.0270 chunk 177 optimal weight: 0.0050 chunk 263 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN B 687 ASN D 687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 25782 Z= 0.196 Angle : 0.706 15.801 34986 Z= 0.344 Chirality : 0.043 0.179 4020 Planarity : 0.005 0.083 4488 Dihedral : 11.568 168.265 3684 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3240 helix: 0.16 (0.13), residues: 1590 sheet: 0.48 (0.30), residues: 366 loop : -0.35 (0.19), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 823 time to evaluate : 3.284 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 outliers start: 37 outliers final: 18 residues processed: 839 average time/residue: 0.4837 time to fit residues: 583.5232 Evaluate side-chains 812 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 794 time to evaluate : 2.826 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2650 time to fit residues: 12.4325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.0470 chunk 60 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 154 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 HIS ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN B 311 ASN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 588 ASN F 701 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 25782 Z= 0.217 Angle : 0.712 14.350 34986 Z= 0.350 Chirality : 0.044 0.174 4020 Planarity : 0.005 0.087 4488 Dihedral : 11.493 164.492 3684 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3240 helix: 0.35 (0.13), residues: 1548 sheet: 0.66 (0.30), residues: 348 loop : -0.43 (0.19), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 819 time to evaluate : 2.965 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 outliers start: 31 outliers final: 15 residues processed: 832 average time/residue: 0.4873 time to fit residues: 583.6321 Evaluate side-chains 821 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 806 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2305 time to fit residues: 10.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.9980 chunk 299 optimal weight: 4.9990 chunk 272 optimal weight: 0.2980 chunk 291 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 275 optimal weight: 0.9980 chunk 289 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN B 311 ASN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 25782 Z= 0.265 Angle : 0.753 14.069 34986 Z= 0.372 Chirality : 0.045 0.176 4020 Planarity : 0.005 0.093 4488 Dihedral : 11.534 159.524 3684 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3240 helix: 0.30 (0.13), residues: 1566 sheet: 0.65 (0.30), residues: 348 loop : -0.46 (0.19), residues: 1326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 828 time to evaluate : 3.459 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 outliers start: 22 outliers final: 14 residues processed: 833 average time/residue: 0.4922 time to fit residues: 588.5214 Evaluate side-chains 820 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 806 time to evaluate : 2.970 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4264 time to fit residues: 14.0135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.8980 chunk 307 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 145 optimal weight: 0.4980 chunk 213 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN B 426 GLN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 25782 Z= 0.225 Angle : 0.769 14.533 34986 Z= 0.375 Chirality : 0.044 0.184 4020 Planarity : 0.006 0.088 4488 Dihedral : 11.455 161.671 3684 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3240 helix: 0.31 (0.13), residues: 1560 sheet: 0.63 (0.30), residues: 348 loop : -0.45 (0.19), residues: 1332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 809 time to evaluate : 3.215 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 outliers start: 13 outliers final: 7 residues processed: 812 average time/residue: 0.5033 time to fit residues: 592.5338 Evaluate side-chains 802 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 795 time to evaluate : 3.089 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2981 time to fit residues: 7.8986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 237 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 257 optimal weight: 0.0470 chunk 107 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 729 GLN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 642 ASN F 426 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118424 restraints weight = 44171.769| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.50 r_work: 0.3384 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 25782 Z= 0.217 Angle : 0.767 15.740 34986 Z= 0.375 Chirality : 0.044 0.184 4020 Planarity : 0.005 0.089 4488 Dihedral : 11.409 165.018 3684 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3240 helix: 0.27 (0.13), residues: 1554 sheet: 0.61 (0.30), residues: 348 loop : -0.43 (0.19), residues: 1338 =============================================================================== Job complete usr+sys time: 8855.79 seconds wall clock time: 158 minutes 35.09 seconds (9515.09 seconds total)