Starting phenix.real_space_refine (version: dev) on Sun May 15 06:29:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/05_2022/5vn3_8713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/05_2022/5vn3_8713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/05_2022/5vn3_8713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/05_2022/5vn3_8713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/05_2022/5vn3_8713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/05_2022/5vn3_8713.pdb" } resolution = 3.7 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= 0.000 sd= 0.010 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 23727 Number of models: 1 Model: "" Number of chains: 21 Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 102, 'PCIS': 1} Chain: "A" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "G" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "N" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 102, 'PCIS': 1} Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "K" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 102, 'PCIS': 1} Chain: "D" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "J" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "M" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 507 Unusual residues: {'BMA': 7, 'NAG': 26, 'MAN': 6} Classifications: {'undetermined': 39} Link IDs: {None: 38} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 39 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 507 Unusual residues: {'BMA': 7, 'NAG': 26, 'MAN': 6} Classifications: {'undetermined': 39} Link IDs: {None: 38} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 39 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 507 Unusual residues: {'BMA': 7, 'NAG': 26, 'MAN': 6} Classifications: {'undetermined': 39} Link IDs: {None: 38} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 39 Time building chain proxies: 13.42, per 1000 atoms: 0.57 Number of scatterers: 23727 At special positions: 0 Unit cell: (192.57, 188.64, 146.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 4860 8.00 N 3936 7.00 C 14808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS G 501 " distance=1.98 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.02 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.01 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS I 501 " distance=2.04 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 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.02 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.01 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 159 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS J 501 " distance=2.09 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.02 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.02 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.01 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.02 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.04 Simple disulfide: pdb=" SG CYS F 130 " - pdb=" SG CYS F 159 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 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=7, symmetry=0 Links applied ALPHA1-2 " MAN G 610 " - " MAN G 611 " " MAN G 611 " - " MAN G 612 " " MAN I 610 " - " MAN I 611 " " MAN I 611 " - " MAN I 612 " " MAN J 610 " - " MAN J 611 " " MAN J 611 " - " MAN J 612 " ALPHA1-3 " BMA G 609 " - " MAN G 610 " " BMA G 626 " - " MAN G 627 " " BMA I 609 " - " MAN I 610 " " BMA I 626 " - " MAN I 627 " " BMA J 609 " - " MAN J 610 " " BMA J 626 " - " MAN J 627 " ALPHA1-6 " BMA G 609 " - " MAN G 613 " " BMA G 616 " - " MAN G 617 " " BMA I 609 " - " MAN I 613 " " BMA I 616 " - " MAN I 617 " " BMA J 609 " - " MAN J 613 " " BMA J 616 " - " MAN J 617 " BETA1-4 " NAG G 602 " - " NAG G 603 " " NAG G 604 " - " NAG G 605 " " NAG G 605 " - " BMA G 606 " " NAG G 607 " - " NAG G 608 " " NAG G 608 " - " BMA G 609 " " NAG G 614 " - " NAG G 615 " " NAG G 615 " - " BMA G 616 " " NAG G 618 " - " NAG G 619 " " NAG G 620 " - " NAG G 621 " " NAG G 624 " - " NAG G 625 " " NAG G 625 " - " BMA G 626 " " NAG G 628 " - " NAG G 629 " " NAG G 629 " - " BMA G 630 " " NAG G 632 " - " NAG G 633 " " NAG G 633 " - " BMA G 634 " " NAG G 635 " - " NAG G 636 " " NAG G 637 " - " NAG G 638 " " NAG G 638 " - " BMA G 639 " " NAG I 602 " - " NAG I 603 " " NAG I 604 " - " NAG I 605 " " NAG I 605 " - " BMA I 606 " " NAG I 607 " - " NAG I 608 " " NAG I 608 " - " BMA I 609 " " NAG I 614 " - " NAG I 615 " " NAG I 615 " - " BMA I 616 " " NAG I 618 " - " NAG I 619 " " NAG I 620 " - " NAG I 621 " " NAG I 624 " - " NAG I 625 " " NAG I 625 " - " BMA I 626 " " NAG I 628 " - " NAG I 629 " " NAG I 629 " - " BMA I 630 " " NAG I 632 " - " NAG I 633 " " NAG I 633 " - " BMA I 634 " " NAG I 635 " - " NAG I 636 " " NAG I 637 " - " NAG I 638 " " NAG I 638 " - " BMA I 639 " " NAG J 602 " - " NAG J 603 " " NAG J 604 " - " NAG J 605 " " NAG J 605 " - " BMA J 606 " " NAG J 607 " - " NAG J 608 " " NAG J 608 " - " BMA J 609 " " NAG J 614 " - " NAG J 615 " " NAG J 615 " - " BMA J 616 " " NAG J 618 " - " NAG J 619 " " NAG J 620 " - " NAG J 621 " " NAG J 624 " - " NAG J 625 " " NAG J 625 " - " BMA J 626 " " NAG J 628 " - " NAG J 629 " " NAG J 629 " - " BMA J 630 " " NAG J 632 " - " NAG J 633 " " NAG J 633 " - " BMA J 634 " " NAG J 635 " - " NAG J 636 " " NAG J 637 " - " NAG J 638 " " NAG J 638 " - " BMA J 639 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 616 " " NAG A 703 " - " ASN A 625 " " NAG A 704 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 616 " " NAG D 703 " - " ASN D 625 " " NAG D 704 " - " ASN D 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 234 " " NAG G 604 " - " ASN G 241 " " NAG G 607 " - " ASN G 262 " " NAG G 614 " - " ASN G 276 " " NAG G 618 " - " ASN G 295 " " NAG G 620 " - " ASN G 332 " " NAG G 622 " - " ASN G 339 " " NAG G 623 " - " ASN G 355 " " NAG G 624 " - " ASN G 362 " " NAG G 628 " - " ASN G 386 " " NAG G 631 " - " ASN G 397 " " NAG G 632 " - " ASN G 413 " " NAG G 635 " - " ASN G 448 " " NAG G 637 " - " ASN G 392 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 234 " " NAG I 604 " - " ASN I 241 " " NAG I 607 " - " ASN I 262 " " NAG I 614 " - " ASN I 276 " " NAG I 618 " - " ASN I 295 " " NAG I 620 " - " ASN I 332 " " NAG I 622 " - " ASN I 339 " " NAG I 623 " - " ASN I 355 " " NAG I 624 " - " ASN I 362 " " NAG I 628 " - " ASN I 386 " " NAG I 631 " - " ASN I 397 " " NAG I 632 " - " ASN I 413 " " NAG I 635 " - " ASN I 448 " " NAG I 637 " - " ASN I 392 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 234 " " NAG J 604 " - " ASN J 241 " " NAG J 607 " - " ASN J 262 " " NAG J 614 " - " ASN J 276 " " NAG J 618 " - " ASN J 295 " " NAG J 620 " - " ASN J 332 " " NAG J 622 " - " ASN J 339 " " NAG J 623 " - " ASN J 355 " " NAG J 624 " - " ASN J 362 " " NAG J 628 " - " ASN J 386 " " NAG J 631 " - " ASN J 397 " " NAG J 632 " - " ASN J 413 " " NAG J 635 " - " ASN J 448 " " NAG J 637 " - " ASN J 392 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 3.6 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 54 sheets defined 17.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 529 through 547 removed outlier: 3.820A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.718A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.733A pdb=" N LYS A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 662 removed outlier: 3.580A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 73 Processing helix chain 'G' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR G 341 " --> pdb=" O ARG G 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.821A pdb=" N THR G 373 " --> pdb=" O PRO G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE G 391 " --> pdb=" O THR G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 481 removed outlier: 3.501A pdb=" N ASN G 478 " --> pdb=" O ASN G 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 removed outlier: 3.820A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.718A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP B 623 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.734A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 662 removed outlier: 3.581A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 73 Processing helix chain 'I' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR I 341 " --> pdb=" O ARG I 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.822A pdb=" N THR I 373 " --> pdb=" O PRO I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE I 391 " --> pdb=" O THR I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 481 removed outlier: 3.500A pdb=" N ASN I 478 " --> pdb=" O ASN I 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 547 removed outlier: 3.821A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 568 Processing helix chain 'D' and resid 569 through 593 removed outlier: 3.719A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 596 No H-bonds generated for 'chain 'D' and resid 594 through 596' Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.734A pdb=" N LYS D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 662 removed outlier: 3.581A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 660 " --> pdb=" O ASN D 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU D 662 " --> pdb=" O GLN D 658 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 73 Processing helix chain 'J' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR J 341 " --> pdb=" O ARG J 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA J 347 " --> pdb=" O GLY J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.821A pdb=" N THR J 373 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE J 391 " --> pdb=" O THR J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 481 removed outlier: 3.500A pdb=" N ASN J 478 " --> pdb=" O ASN J 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER J 481 " --> pdb=" O ASP J 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'M' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.585A pdb=" N ALA L 25 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL G 36 " --> pdb=" O THR G 499 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR G 499 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL G 38 " --> pdb=" O ALA G 497 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA G 497 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR G 40 " --> pdb=" O GLY G 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY G 495 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL G 44 " --> pdb=" O ILE G 491 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE G 491 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.557A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 357 through 361 Processing sheet with id=AA9, first strand: chain 'G' and resid 374 through 378 Processing sheet with id=AB1, first strand: chain 'G' and resid 423 through 425 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.076A pdb=" N LYS C 2 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN C 40 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY C 99 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN C 112 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 148 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL C 168 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 37 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 37 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.586A pdb=" N ALA N 25 " --> pdb=" O ALA N 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA N 34 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL I 36 " --> pdb=" O THR I 499 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR I 499 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL I 38 " --> pdb=" O ALA I 497 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA I 497 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR I 40 " --> pdb=" O GLY I 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY I 495 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL I 44 " --> pdb=" O ILE I 491 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE I 491 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'I' and resid 84 through 85 removed outlier: 3.556A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N VAL I 292 " --> pdb=" O SER I 446 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N SER I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 357 through 361 Processing sheet with id=AC9, first strand: chain 'I' and resid 374 through 378 Processing sheet with id=AD1, first strand: chain 'I' and resid 423 through 425 Processing sheet with id=AD2, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.076A pdb=" N LYS E 2 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AD4, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN E 40 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY E 99 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN E 112 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN E 148 " --> pdb=" O GLN E 112 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL E 168 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE K 91 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE K 91 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.585A pdb=" N ALA O 25 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA O 69 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA O 34 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN O 89 " --> pdb=" O ALA O 34 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL J 36 " --> pdb=" O THR J 499 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR J 499 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL J 38 " --> pdb=" O ALA J 497 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA J 497 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR J 40 " --> pdb=" O GLY J 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY J 495 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL J 44 " --> pdb=" O ILE J 491 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE J 491 " --> pdb=" O VAL J 44 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AE5, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.557A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS J 487 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.502A pdb=" N VAL J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN J 295 " --> pdb=" O ASN J 332 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.502A pdb=" N VAL J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 357 through 361 Processing sheet with id=AE9, first strand: chain 'J' and resid 374 through 378 Processing sheet with id=AF1, first strand: chain 'J' and resid 423 through 425 Processing sheet with id=AF2, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.077A pdb=" N LYS F 2 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AF4, first strand: chain 'F' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN F 40 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY F 99 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN F 112 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN F 148 " --> pdb=" O GLN F 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL F 168 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL M 37 " --> pdb=" O PHE M 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL M 37 " --> pdb=" O PHE M 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1566 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: 8.17 Time building geometry restraints manager: 13.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7422 1.34 - 1.46: 5788 1.46 - 1.58: 10792 1.58 - 1.70: 1 1.70 - 1.82: 159 Bond restraints: 24162 Sorted by residual: bond pdb=" C GLN L 38 " pdb=" N LYS L 39 " ideal model delta sigma weight residual 1.333 1.238 0.094 2.74e-02 1.33e+03 1.18e+01 bond pdb=" C GLN O 38 " pdb=" N LYS O 39 " ideal model delta sigma weight residual 1.333 1.238 0.094 2.74e-02 1.33e+03 1.18e+01 bond pdb=" C GLN N 38 " pdb=" N LYS N 39 " ideal model delta sigma weight residual 1.333 1.239 0.093 2.74e-02 1.33e+03 1.16e+01 bond pdb=" CB TRP I 45 " pdb=" CG TRP I 45 " ideal model delta sigma weight residual 1.498 1.419 0.079 3.10e-02 1.04e+03 6.52e+00 bond pdb=" CB TRP G 45 " pdb=" CG TRP G 45 " ideal model delta sigma weight residual 1.498 1.420 0.078 3.10e-02 1.04e+03 6.41e+00 ... (remaining 24157 not shown) Histogram of bond angle deviations from ideal: 97.38 - 104.74: 381 104.74 - 112.11: 12814 112.11 - 119.47: 8059 119.47 - 126.83: 11147 126.83 - 134.20: 389 Bond angle restraints: 32790 Sorted by residual: angle pdb=" C ASN G 300 " pdb=" N ASN G 301 " pdb=" CA ASN G 301 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C ASN J 300 " pdb=" N ASN J 301 " pdb=" CA ASN J 301 " ideal model delta sigma weight residual 121.54 133.07 -11.53 1.91e+00 2.74e-01 3.64e+01 angle pdb=" C ASN I 300 " pdb=" N ASN I 301 " pdb=" CA ASN I 301 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.62e+01 angle pdb=" N ASN I 301 " pdb=" CA ASN I 301 " pdb=" C ASN I 301 " ideal model delta sigma weight residual 110.80 120.95 -10.15 2.13e+00 2.20e-01 2.27e+01 angle pdb=" N ASN G 301 " pdb=" CA ASN G 301 " pdb=" C ASN G 301 " ideal model delta sigma weight residual 110.80 120.90 -10.10 2.13e+00 2.20e-01 2.25e+01 ... (remaining 32785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 13784 15.57 - 31.14: 514 31.14 - 46.71: 165 46.71 - 62.28: 15 62.28 - 77.85: 24 Dihedral angle restraints: 14502 sinusoidal: 6420 harmonic: 8082 Sorted by residual: dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.85 77.85 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.85 77.85 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.84 77.84 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 14499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3264 0.072 - 0.144: 704 0.144 - 0.216: 114 0.216 - 0.289: 7 0.289 - 0.361: 3 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CB ILE B 603 " pdb=" CA ILE B 603 " pdb=" CG1 ILE B 603 " pdb=" CG2 ILE B 603 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE D 603 " pdb=" CA ILE D 603 " pdb=" CG1 ILE D 603 " pdb=" CG2 ILE D 603 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE A 603 " pdb=" CA ILE A 603 " pdb=" CG1 ILE A 603 " pdb=" CG2 ILE A 603 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 4089 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 625 " 0.024 2.00e-02 2.50e+03 2.36e-02 6.97e+00 pdb=" CG ASN A 625 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 625 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 625 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 276 " 0.023 2.00e-02 2.50e+03 2.29e-02 6.55e+00 pdb=" CG ASN G 276 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN G 276 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN G 276 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG G 614 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 276 " 0.022 2.00e-02 2.50e+03 2.23e-02 6.24e+00 pdb=" CG ASN I 276 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN I 276 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN I 276 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG I 614 " 0.028 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4503 2.77 - 3.30: 21149 3.30 - 3.83: 37189 3.83 - 4.37: 41954 4.37 - 4.90: 73821 Nonbonded interactions: 178616 Sorted by model distance: nonbonded pdb=" O GLY J 441 " pdb=" O6 MAN J 611 " model vdw 2.235 2.440 nonbonded pdb=" O GLY I 441 " pdb=" O6 MAN I 611 " model vdw 2.247 2.440 nonbonded pdb=" O CYS D 604 " pdb=" OG1 THR J 37 " model vdw 2.256 2.440 nonbonded pdb=" NE2 GLN L 38 " pdb=" O LYS L 39 " model vdw 2.294 2.520 nonbonded pdb=" NE2 GLN O 38 " pdb=" O LYS O 39 " model vdw 2.295 2.520 ... (remaining 178611 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' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 14808 2.51 5 N 3936 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.030 Extract box with map and model: 6.270 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.210 Process input model: 64.180 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.009 0.094 24162 Z= 0.609 Angle : 1.126 11.544 32790 Z= 0.642 Chirality : 0.060 0.361 4092 Planarity : 0.006 0.062 4011 Dihedral : 9.180 71.386 9156 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.76 % Favored : 88.80 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -5.03 (0.12), residues: 2760 helix: -4.37 (0.10), residues: 444 sheet: -2.51 (0.18), residues: 720 loop : -3.56 (0.12), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 514 time to evaluate : 2.796 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 outliers start: 3 outliers final: 0 residues processed: 514 average time/residue: 0.4008 time to fit residues: 304.3771 Evaluate side-chains 271 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 247 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 197 ASN G 308 HIS ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 462 GLN C 25 GLN C 163 GLN H 82BASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN B 653 GLN I 103 GLN I 197 ASN I 377 ASN ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN I 462 GLN E 25 GLN E 163 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 GLN J 197 ASN J 377 ASN ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 GLN F 25 GLN F 163 GLN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 24162 Z= 0.212 Angle : 0.663 10.083 32790 Z= 0.348 Chirality : 0.044 0.220 4092 Planarity : 0.005 0.069 4011 Dihedral : 5.513 63.517 3918 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.26 % Favored : 91.52 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -3.88 (0.14), residues: 2760 helix: -2.10 (0.20), residues: 423 sheet: -1.99 (0.18), residues: 768 loop : -3.14 (0.13), residues: 1569 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 339 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 15 residues processed: 367 average time/residue: 0.3280 time to fit residues: 191.9102 Evaluate side-chains 265 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 250 time to evaluate : 2.833 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2339 time to fit residues: 10.0874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 chunk 246 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 24162 Z= 0.233 Angle : 0.630 7.792 32790 Z= 0.325 Chirality : 0.044 0.270 4092 Planarity : 0.004 0.079 4011 Dihedral : 5.496 58.371 3918 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.70 % Favored : 91.09 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.28 (0.14), residues: 2760 helix: -1.15 (0.23), residues: 456 sheet: -1.68 (0.18), residues: 765 loop : -2.87 (0.14), residues: 1539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 304 average time/residue: 0.3200 time to fit residues: 158.8851 Evaluate side-chains 264 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 2.848 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.2057 time to fit residues: 11.6978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100HASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 24162 Z= 0.377 Angle : 0.692 11.551 32790 Z= 0.352 Chirality : 0.045 0.353 4092 Planarity : 0.005 0.093 4011 Dihedral : 5.766 51.271 3918 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.46 % Favored : 90.33 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.05 (0.15), residues: 2760 helix: -0.91 (0.24), residues: 456 sheet: -1.48 (0.19), residues: 720 loop : -2.73 (0.14), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 254 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 31 residues processed: 280 average time/residue: 0.3219 time to fit residues: 147.5096 Evaluate side-chains 260 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 2.726 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 1 residues processed: 31 average time/residue: 0.2100 time to fit residues: 15.7853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24162 Z= 0.207 Angle : 0.592 10.231 32790 Z= 0.302 Chirality : 0.043 0.329 4092 Planarity : 0.004 0.069 4011 Dihedral : 5.557 54.814 3918 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.90 % Favored : 91.88 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.15), residues: 2760 helix: -0.49 (0.24), residues: 459 sheet: -1.32 (0.18), residues: 747 loop : -2.56 (0.14), residues: 1554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 277 average time/residue: 0.3224 time to fit residues: 147.4240 Evaluate side-chains 241 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 234 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2100 time to fit residues: 6.5514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 20.0000 chunk 237 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 219 optimal weight: 0.0470 chunk 122 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100HASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24162 Z= 0.187 Angle : 0.579 10.774 32790 Z= 0.293 Chirality : 0.042 0.319 4092 Planarity : 0.004 0.058 4011 Dihedral : 5.404 57.095 3918 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.75 % Favored : 92.03 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2760 helix: -0.07 (0.25), residues: 456 sheet: -1.08 (0.19), residues: 750 loop : -2.40 (0.14), residues: 1554 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 272 average time/residue: 0.3190 time to fit residues: 142.8230 Evaluate side-chains 250 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2334 time to fit residues: 9.4893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 150 optimal weight: 0.0770 chunk 192 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 164 optimal weight: 30.0000 chunk 160 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS I 197 ASN ** I 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 24162 Z= 0.347 Angle : 0.660 12.446 32790 Z= 0.335 Chirality : 0.044 0.348 4092 Planarity : 0.005 0.095 4011 Dihedral : 5.670 54.152 3918 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.67 % Favored : 90.11 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.15), residues: 2760 helix: -0.29 (0.25), residues: 456 sheet: -1.02 (0.20), residues: 675 loop : -2.46 (0.14), residues: 1629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 240 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 251 average time/residue: 0.3330 time to fit residues: 135.4179 Evaluate side-chains 240 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 224 time to evaluate : 2.821 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2583 time to fit residues: 11.2812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 79 optimal weight: 0.0670 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 167 optimal weight: 40.0000 chunk 179 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 301 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 24162 Z= 0.236 Angle : 0.607 12.381 32790 Z= 0.306 Chirality : 0.043 0.338 4092 Planarity : 0.004 0.072 4011 Dihedral : 5.564 55.961 3918 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.15 % Favored : 91.63 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2760 helix: -0.05 (0.25), residues: 456 sheet: -0.93 (0.20), residues: 708 loop : -2.38 (0.14), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 237 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 241 average time/residue: 0.3140 time to fit residues: 124.6301 Evaluate side-chains 234 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 228 time to evaluate : 2.800 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2216 time to fit residues: 6.0897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 9.9990 chunk 252 optimal weight: 0.7980 chunk 229 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 192 optimal weight: 0.0980 chunk 75 optimal weight: 0.0470 chunk 221 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 ASN ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 24162 Z= 0.179 Angle : 0.580 12.500 32790 Z= 0.292 Chirality : 0.042 0.321 4092 Planarity : 0.004 0.059 4011 Dihedral : 5.338 56.827 3918 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.50 % Favored : 92.28 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2760 helix: 0.47 (0.26), residues: 447 sheet: -0.75 (0.20), residues: 702 loop : -2.20 (0.14), residues: 1611 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 264 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 267 average time/residue: 0.3135 time to fit residues: 137.8036 Evaluate side-chains 236 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 230 time to evaluate : 2.837 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2285 time to fit residues: 6.3295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 10.0000 chunk 259 optimal weight: 30.0000 chunk 158 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 167 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 GLN ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.070 24162 Z= 0.517 Angle : 0.783 14.226 32790 Z= 0.393 Chirality : 0.047 0.374 4092 Planarity : 0.005 0.065 4011 Dihedral : 6.054 54.122 3918 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.54 % Favored : 89.24 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.15), residues: 2760 helix: -0.46 (0.24), residues: 453 sheet: -1.00 (0.19), residues: 738 loop : -2.39 (0.14), residues: 1569 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 2.859 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 226 average time/residue: 0.3201 time to fit residues: 118.9604 Evaluate side-chains 219 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 2.753 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2089 time to fit residues: 5.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 216 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.097042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072989 restraints weight = 68303.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073925 restraints weight = 42947.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074070 restraints weight = 34218.081| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 24162 Z= 0.211 Angle : 0.618 13.318 32790 Z= 0.311 Chirality : 0.043 0.332 4092 Planarity : 0.004 0.058 4011 Dihedral : 5.620 58.484 3918 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.39 % Favored : 92.39 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.16), residues: 2760 helix: 0.12 (0.25), residues: 456 sheet: -0.77 (0.20), residues: 708 loop : -2.24 (0.14), residues: 1596 =============================================================================== Job complete usr+sys time: 3960.26 seconds wall clock time: 73 minutes 54.18 seconds (4434.18 seconds total)