Starting phenix.real_space_refine on Wed Mar 20 23:28:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/03_2024/6d04_7784_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/03_2024/6d04_7784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/03_2024/6d04_7784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/03_2024/6d04_7784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/03_2024/6d04_7784_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d04_7784/03_2024/6d04_7784_updated.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 142 5.16 5 C 18252 2.51 5 N 4850 2.21 5 O 5498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ARG 568": "NH1" <-> "NH2" Residue "C TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 522": "NH1" <-> "NH2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 632": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 242": "NH1" <-> "NH2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 468": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 457} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 457} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.56, per 1000 atoms: 0.51 Number of scatterers: 28748 At special positions: 0 Unit cell: (168.75, 148.5, 166.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 142 16.00 O 5498 8.00 N 4850 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.02 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.02 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.03 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.02 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.02 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.02 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.03 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.03 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.04 Simple disulfide: pdb=" SG CYS F 240 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 316 " distance=2.03 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=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG B 802 " - " ASN B 251 " " NAG C 707 " - " ASN C 611 " " NAG D 707 " - " ASN D 611 " " NAG G 1 " - " ASN A 317 " " NAG H 1 " - " ASN A 727 " " NAG I 1 " - " ASN B 317 " " NAG J 1 " - " ASN B 727 " " NAG K 1 " - " ASN C 413 " " NAG L 1 " - " ASN D 413 " Time building additional restraints: 10.94 Conformation dependent library (CDL) restraints added in 5.1 seconds 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 20 sheets defined 44.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.71 Creating SS restraints... Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.034A pdb=" N ARG A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.522A pdb=" N ASN A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.655A pdb=" N LYS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 438 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 500 through 511 removed outlier: 5.156A pdb=" N THR A 504 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 542 through 545 No H-bonds generated for 'chain 'A' and resid 542 through 545' Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 611 through 634 removed outlier: 3.799A pdb=" N TYR A 614 " --> pdb=" O TYR A 611 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 618 " --> pdb=" O ASN A 615 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 622 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 623 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 629 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA A 630 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 661 Processing helix chain 'A' and resid 669 through 680 removed outlier: 3.537A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 709 through 720 removed outlier: 4.125A pdb=" N LEU A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 749 Processing helix chain 'B' and resid 124 through 135 removed outlier: 4.034A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.521A pdb=" N ASN B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.654A pdb=" N LYS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 438 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 471 through 474 No H-bonds generated for 'chain 'B' and resid 471 through 474' Processing helix chain 'B' and resid 500 through 511 removed outlier: 5.155A pdb=" N THR B 504 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 542 through 545 No H-bonds generated for 'chain 'B' and resid 542 through 545' Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 611 through 634 removed outlier: 3.799A pdb=" N TYR B 614 " --> pdb=" O TYR B 611 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 618 " --> pdb=" O ASN B 615 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 622 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 623 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN B 627 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 629 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA B 630 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 632 " --> pdb=" O ARG B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 661 Processing helix chain 'B' and resid 669 through 680 removed outlier: 3.538A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 709 through 720 removed outlier: 4.125A pdb=" N LEU B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 749 Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 188 through 196 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.833A pdb=" N HIS C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 314 No H-bonds generated for 'chain 'C' and resid 311 through 314' Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 374 through 383 removed outlier: 3.519A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 removed outlier: 3.808A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 471 removed outlier: 3.711A pdb=" N LEU C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 495 No H-bonds generated for 'chain 'C' and resid 493 through 495' Processing helix chain 'C' and resid 516 through 526 removed outlier: 3.602A pdb=" N ALA C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 594 through 608 removed outlier: 4.026A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 651 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.748A pdb=" N LEU C 662 " --> pdb=" O ALA C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 675 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 64 through 67 No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 188 through 196 Processing helix chain 'D' and resid 209 through 213 Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 260 through 274 removed outlier: 3.832A pdb=" N HIS D 273 " --> pdb=" O GLN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 314 No H-bonds generated for 'chain 'D' and resid 311 through 314' Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 352 through 361 Processing helix chain 'D' and resid 374 through 383 removed outlier: 3.519A pdb=" N ALA D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 402 removed outlier: 3.807A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 removed outlier: 3.711A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 516 through 526 removed outlier: 3.604A pdb=" N ALA D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 594 through 608 removed outlier: 4.025A pdb=" N LEU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.748A pdb=" N LEU D 662 " --> pdb=" O ALA D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 675 Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 217 through 239 Processing helix chain 'E' and resid 241 through 254 Processing helix chain 'E' and resid 258 through 261 No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 267 through 307 removed outlier: 3.564A pdb=" N LYS E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 334 removed outlier: 4.569A pdb=" N LYS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 361 removed outlier: 3.594A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 407 Processing helix chain 'E' and resid 416 through 476 removed outlier: 3.620A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY E 463 " --> pdb=" O GLY E 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG E 468 " --> pdb=" O HIS E 464 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 511 removed outlier: 5.466A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 565 removed outlier: 4.035A pdb=" N ASP E 524 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 632 removed outlier: 4.170A pdb=" N ASN E 591 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER E 593 " --> pdb=" O TYR E 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 217 through 239 Processing helix chain 'F' and resid 241 through 254 Processing helix chain 'F' and resid 258 through 261 No H-bonds generated for 'chain 'F' and resid 258 through 261' Processing helix chain 'F' and resid 267 through 307 removed outlier: 3.564A pdb=" N LYS F 288 " --> pdb=" O CYS F 284 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS F 291 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 334 removed outlier: 4.569A pdb=" N LYS F 326 " --> pdb=" O PHE F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 361 removed outlier: 3.594A pdb=" N LYS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 407 Processing helix chain 'F' and resid 416 through 476 removed outlier: 3.620A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY F 463 " --> pdb=" O GLY F 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG F 468 " --> pdb=" O HIS F 464 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP F 474 " --> pdb=" O SER F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 511 removed outlier: 5.466A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 565 removed outlier: 4.034A pdb=" N ASP F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 632 removed outlier: 4.170A pdb=" N ASN F 591 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE F 592 " --> pdb=" O SER F 588 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER F 593 " --> pdb=" O TYR F 589 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 180 through 193 removed outlier: 9.057A pdb=" N GLU A 398 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ILE A 449 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 12.830A pdb=" N ASP A 400 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 14.748A pdb=" N ALA A 451 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 15.233A pdb=" N TYR A 402 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 16.415A pdb=" N TRP A 453 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 14.836A pdb=" N VAL A 404 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 406 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 226 through 230 removed outlier: 5.871A pdb=" N ILE A 202 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU A 212 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.183A pdb=" N ILE A 254 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY A 278 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 257 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 280 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE A 281 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN A 335 " --> pdb=" O ILE A 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 180 through 193 removed outlier: 9.058A pdb=" N GLU B 398 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ILE B 449 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 12.830A pdb=" N ASP B 400 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 14.748A pdb=" N ALA B 451 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 15.232A pdb=" N TYR B 402 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 16.415A pdb=" N TRP B 453 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 14.835A pdb=" N VAL B 404 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 406 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 226 through 230 removed outlier: 3.501A pdb=" N GLU B 214 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE B 202 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 212 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.182A pdb=" N ILE B 254 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY B 278 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL B 257 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 280 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE B 281 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN B 335 " --> pdb=" O ILE B 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 5 through 10 removed outlier: 6.272A pdb=" N SER C 36 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TRP C 8 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 38 " --> pdb=" O TRP C 8 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA C 10 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 40 " --> pdb=" O ALA C 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.932A pdb=" N VAL C 60 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 81 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA C 253 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 244 through 246 removed outlier: 3.894A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 224 through 226 Processing sheet with id= K, first strand: chain 'C' and resid 342 through 347 Processing sheet with id= L, first strand: chain 'C' and resid 388 through 391 removed outlier: 3.680A pdb=" N LEU C 408 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR C 589 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 531 through 534 removed outlier: 5.128A pdb=" N ALA C 430 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 562 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 569 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.272A pdb=" N SER D 36 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TRP D 8 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA D 38 " --> pdb=" O TRP D 8 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA D 10 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 40 " --> pdb=" O ALA D 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.933A pdb=" N VAL D 60 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 81 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA D 253 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 244 through 246 removed outlier: 3.894A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 224 through 226 Processing sheet with id= R, first strand: chain 'D' and resid 342 through 347 Processing sheet with id= S, first strand: chain 'D' and resid 388 through 391 removed outlier: 3.680A pdb=" N LEU D 408 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR D 589 " --> pdb=" O PRO D 406 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 531 through 534 removed outlier: 5.129A pdb=" N ALA D 430 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 562 " --> pdb=" O ALA D 430 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS D 569 " --> pdb=" O LEU D 561 " (cutoff:3.500A) 1229 hydrogen bonds defined for protein. 3501 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: 9.60 Time building geometry restraints manager: 11.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8531 1.34 - 1.46: 6384 1.46 - 1.58: 14253 1.58 - 1.70: 0 1.70 - 1.83: 192 Bond restraints: 29360 Sorted by residual: bond pdb=" CA ARG B 155 " pdb=" CB ARG B 155 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.46e-02 4.69e+03 7.32e+00 bond pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 1.524 1.563 -0.039 1.46e-02 4.69e+03 7.13e+00 bond pdb=" C1 NAG C 707 " pdb=" O5 NAG C 707 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" N ASN B 236 " pdb=" CA ASN B 236 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.79e+00 bond pdb=" N ASN A 236 " pdb=" CA ASN A 236 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.71e+00 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.71: 402 104.71 - 112.09: 14137 112.09 - 119.47: 10211 119.47 - 126.85: 14557 126.85 - 134.23: 357 Bond angle restraints: 39664 Sorted by residual: angle pdb=" CA TYR E 422 " pdb=" CB TYR E 422 " pdb=" CG TYR E 422 " ideal model delta sigma weight residual 113.90 127.79 -13.89 1.80e+00 3.09e-01 5.96e+01 angle pdb=" CA TYR F 422 " pdb=" CB TYR F 422 " pdb=" CG TYR F 422 " ideal model delta sigma weight residual 113.90 127.76 -13.86 1.80e+00 3.09e-01 5.93e+01 angle pdb=" C GLY C 502 " pdb=" N LEU C 503 " pdb=" CA LEU C 503 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY D 502 " pdb=" N LEU D 503 " pdb=" CA LEU D 503 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C ASN C 461 " pdb=" N ILE C 462 " pdb=" CA ILE C 462 " ideal model delta sigma weight residual 120.24 123.28 -3.04 6.30e-01 2.52e+00 2.32e+01 ... (remaining 39659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 17249 21.89 - 43.78: 632 43.78 - 65.67: 109 65.67 - 87.56: 32 87.56 - 109.46: 20 Dihedral angle restraints: 18042 sinusoidal: 7570 harmonic: 10472 Sorted by residual: dihedral pdb=" CA GLN F 317 " pdb=" C GLN F 317 " pdb=" N THR F 318 " pdb=" CA THR F 318 " ideal model delta harmonic sigma weight residual 180.00 92.36 87.64 0 5.00e+00 4.00e-02 3.07e+02 dihedral pdb=" CA GLN E 317 " pdb=" C GLN E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta harmonic sigma weight residual 180.00 92.41 87.59 0 5.00e+00 4.00e-02 3.07e+02 dihedral pdb=" CA ASP F 407 " pdb=" C ASP F 407 " pdb=" N GLY F 408 " pdb=" CA GLY F 408 " ideal model delta harmonic sigma weight residual -180.00 -93.39 -86.61 0 5.00e+00 4.00e-02 3.00e+02 ... (remaining 18039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 4324 0.187 - 0.374: 22 0.374 - 0.561: 4 0.561 - 0.748: 2 0.748 - 0.934: 2 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 727 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 727 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 251 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 4351 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 422 " 0.049 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR F 422 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR F 422 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 422 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 422 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 422 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 422 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 422 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 422 " -0.049 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR E 422 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR E 422 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 422 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 422 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 422 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 422 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 422 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 251 " -0.035 2.00e-02 2.50e+03 3.27e-02 1.34e+01 pdb=" CG ASN B 251 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 251 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 251 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG B 802 " -0.035 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 201 2.58 - 3.16: 22985 3.16 - 3.74: 43570 3.74 - 4.32: 60002 4.32 - 4.90: 97829 Nonbonded interactions: 224587 Sorted by model distance: nonbonded pdb="FE FE D 703 " pdb=" O3 CO3 D 704 " model vdw 2.001 2.260 nonbonded pdb="FE FE C 703 " pdb=" O3 CO3 C 704 " model vdw 2.012 2.260 nonbonded pdb=" OD1 ASP D 63 " pdb="FE FE D 703 " model vdw 2.035 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.039 2.260 nonbonded pdb=" OD1 ASP C 63 " pdb="FE FE C 703 " model vdw 2.043 2.260 ... (remaining 224582 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.220 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 73.950 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 29360 Z= 0.528 Angle : 1.073 13.894 39664 Z= 0.606 Chirality : 0.062 0.934 4354 Planarity : 0.007 0.071 5106 Dihedral : 12.378 109.455 11164 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.21 % Allowed : 6.30 % Favored : 92.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.02 (0.11), residues: 3560 helix: -2.00 (0.10), residues: 1672 sheet: -1.14 (0.26), residues: 336 loop : -2.07 (0.13), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP D 358 HIS 0.011 0.002 HIS D 585 PHE 0.037 0.003 PHE A 176 TYR 0.069 0.003 TYR E 422 ARG 0.023 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 394 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9117 (pp) cc_final: 0.8822 (pp) REVERT: A 510 MET cc_start: 0.8501 (mtp) cc_final: 0.8251 (mtm) REVERT: A 570 MET cc_start: 0.8531 (ttm) cc_final: 0.8230 (ttm) REVERT: A 574 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (pttm) REVERT: A 671 MET cc_start: 0.8622 (mmm) cc_final: 0.8290 (mmt) REVERT: B 126 ASP cc_start: 0.8253 (t70) cc_final: 0.7698 (t0) REVERT: C 309 MET cc_start: 0.8719 (ttm) cc_final: 0.8412 (mtp) REVERT: C 367 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7833 (mt-10) REVERT: C 477 ASP cc_start: 0.7388 (p0) cc_final: 0.6827 (t0) REVERT: C 514 TYR cc_start: 0.7794 (m-10) cc_final: 0.7373 (m-80) REVERT: D 309 MET cc_start: 0.8835 (ttm) cc_final: 0.8457 (mtp) REVERT: D 514 TYR cc_start: 0.7757 (m-10) cc_final: 0.7307 (m-80) REVERT: E 324 MET cc_start: 0.7810 (mmm) cc_final: 0.6493 (tpp) REVERT: E 596 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6688 (tm-30) REVERT: E 608 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8599 (mm) REVERT: F 205 PHE cc_start: 0.8483 (t80) cc_final: 0.8196 (t80) REVERT: F 414 VAL cc_start: 0.6230 (m) cc_final: 0.5935 (m) REVERT: F 508 GLU cc_start: 0.7659 (tt0) cc_final: 0.7434 (tp30) REVERT: F 631 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6670 (tp30) outliers start: 38 outliers final: 4 residues processed: 428 average time/residue: 0.4448 time to fit residues: 288.5707 Evaluate side-chains 145 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain E residue 608 ILE Chi-restraints excluded: chain F residue 600 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 197 GLN A 236 ASN A 275 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 640 GLN A 715 ASN B 148 ASN B 197 GLN B 236 ASN B 275 ASN B 401 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 ASN B 640 GLN B 715 ASN B 721 GLN C 25 HIS C 55 ASN C 300 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 ASN D 55 ASN D 300 HIS ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 GLN D 618 ASN E 231 ASN E 252 ASN E 292 ASN E 346 GLN E 364 GLN E 397 HIS E 444 ASN E 456 ASN E 527 ASN F 231 ASN F 252 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN F 397 HIS F 444 ASN F 456 ASN F 483 ASN F 527 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 29360 Z= 0.377 Angle : 0.716 12.105 39664 Z= 0.377 Chirality : 0.048 0.602 4354 Planarity : 0.005 0.057 5106 Dihedral : 8.521 81.477 4221 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 2.91 % Allowed : 9.75 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.26 (0.13), residues: 3560 helix: -0.05 (0.12), residues: 1674 sheet: -0.93 (0.26), residues: 346 loop : -1.64 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 740 HIS 0.007 0.002 HIS E 222 PHE 0.039 0.002 PHE E 521 TYR 0.051 0.002 TYR F 422 ARG 0.008 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 139 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8257 (mtp) cc_final: 0.7303 (ttm) REVERT: A 574 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8076 (pttm) REVERT: A 583 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 635 MET cc_start: 0.9262 (mtm) cc_final: 0.8918 (mtm) REVERT: A 671 MET cc_start: 0.8772 (mmm) cc_final: 0.8351 (mmt) REVERT: B 126 ASP cc_start: 0.8107 (t70) cc_final: 0.7723 (t0) REVERT: B 198 ASN cc_start: 0.9219 (OUTLIER) cc_final: 0.8938 (p0) REVERT: B 714 GLU cc_start: 0.8268 (tp30) cc_final: 0.8067 (tt0) REVERT: C 62 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8432 (pp) REVERT: C 309 MET cc_start: 0.8826 (ttm) cc_final: 0.8515 (mtp) REVERT: C 499 MET cc_start: 0.8385 (ptm) cc_final: 0.8000 (ptm) REVERT: C 514 TYR cc_start: 0.7844 (m-10) cc_final: 0.7222 (m-80) REVERT: C 538 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8409 (p) REVERT: D 62 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8622 (pp) REVERT: D 309 MET cc_start: 0.8822 (ttm) cc_final: 0.8502 (mtp) REVERT: D 499 MET cc_start: 0.8466 (ptm) cc_final: 0.7901 (ptm) REVERT: D 514 TYR cc_start: 0.7842 (m-10) cc_final: 0.7311 (m-80) REVERT: D 538 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8459 (p) REVERT: E 255 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7377 (pt0) REVERT: E 279 GLU cc_start: 0.7650 (mp0) cc_final: 0.7079 (mp0) REVERT: E 346 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8168 (pp30) REVERT: F 205 PHE cc_start: 0.8508 (t80) cc_final: 0.8226 (t80) REVERT: F 508 GLU cc_start: 0.7667 (tt0) cc_final: 0.7442 (tp30) outliers start: 91 outliers final: 43 residues processed: 219 average time/residue: 0.3943 time to fit residues: 140.6506 Evaluate side-chains 156 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 105 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 322 optimal weight: 5.9990 chunk 347 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 319 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN B 483 ASN C 245 GLN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29360 Z= 0.333 Angle : 0.640 12.119 39664 Z= 0.334 Chirality : 0.047 0.581 4354 Planarity : 0.004 0.047 5106 Dihedral : 7.506 71.273 4215 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.07 % Allowed : 10.90 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 3560 helix: 0.63 (0.12), residues: 1658 sheet: -0.96 (0.27), residues: 358 loop : -1.44 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 740 HIS 0.006 0.001 HIS A 699 PHE 0.022 0.002 PHE C 22 TYR 0.038 0.002 TYR F 422 ARG 0.005 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 121 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 635 MET cc_start: 0.9338 (mtm) cc_final: 0.9034 (mtm) REVERT: B 126 ASP cc_start: 0.8079 (t70) cc_final: 0.7667 (t0) REVERT: B 198 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8914 (p0) REVERT: B 263 THR cc_start: 0.9092 (m) cc_final: 0.8884 (p) REVERT: B 714 GLU cc_start: 0.8300 (tp30) cc_final: 0.8042 (tt0) REVERT: C 62 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8486 (pp) REVERT: C 309 MET cc_start: 0.8812 (ttm) cc_final: 0.8492 (mtp) REVERT: C 499 MET cc_start: 0.8603 (ptm) cc_final: 0.8233 (ptm) REVERT: C 514 TYR cc_start: 0.7943 (m-10) cc_final: 0.7218 (m-80) REVERT: D 62 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8543 (pp) REVERT: D 309 MET cc_start: 0.8806 (ttm) cc_final: 0.8470 (mtp) REVERT: D 499 MET cc_start: 0.8555 (ptm) cc_final: 0.8046 (ptm) REVERT: D 514 TYR cc_start: 0.7949 (m-10) cc_final: 0.7283 (m-80) REVERT: E 205 PHE cc_start: 0.8297 (t80) cc_final: 0.7824 (t80) REVERT: E 279 GLU cc_start: 0.7663 (mp0) cc_final: 0.6815 (mp0) REVERT: E 352 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8936 (mt) REVERT: E 357 MET cc_start: 0.7264 (mmm) cc_final: 0.7012 (mmm) REVERT: F 205 PHE cc_start: 0.8360 (t80) cc_final: 0.7957 (t80) REVERT: F 335 MET cc_start: 0.6462 (tpt) cc_final: 0.6201 (tpt) REVERT: F 352 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8992 (mt) REVERT: F 422 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7790 (m-80) outliers start: 96 outliers final: 56 residues processed: 206 average time/residue: 0.3664 time to fit residues: 127.4154 Evaluate side-chains 163 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 100 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 chunk 323 optimal weight: 6.9990 chunk 342 optimal weight: 0.1980 chunk 168 optimal weight: 0.1980 chunk 306 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 212 HIS F 252 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29360 Z= 0.165 Angle : 0.549 12.594 39664 Z= 0.284 Chirality : 0.043 0.610 4354 Planarity : 0.003 0.043 5106 Dihedral : 6.806 69.110 4210 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 2.49 % Allowed : 12.34 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3560 helix: 1.21 (0.12), residues: 1652 sheet: -0.72 (0.28), residues: 330 loop : -1.29 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 PHE 0.015 0.001 PHE C 22 TYR 0.031 0.001 TYR F 422 ARG 0.004 0.000 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 131 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8239 (mtp) cc_final: 0.7527 (ttm) REVERT: A 635 MET cc_start: 0.9307 (mtm) cc_final: 0.9041 (mtm) REVERT: B 126 ASP cc_start: 0.7764 (t70) cc_final: 0.7391 (t0) REVERT: B 263 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 112 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8769 (tm) REVERT: C 309 MET cc_start: 0.8788 (ttm) cc_final: 0.8435 (mtp) REVERT: C 367 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8007 (mm-30) REVERT: C 499 MET cc_start: 0.8515 (ptm) cc_final: 0.8031 (ptm) REVERT: C 514 TYR cc_start: 0.8017 (m-10) cc_final: 0.7248 (m-80) REVERT: D 112 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8953 (tm) REVERT: D 309 MET cc_start: 0.8680 (ttm) cc_final: 0.8384 (mtp) REVERT: D 338 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: D 499 MET cc_start: 0.8655 (ptm) cc_final: 0.8183 (ptm) REVERT: D 514 TYR cc_start: 0.7955 (m-10) cc_final: 0.7232 (m-80) REVERT: D 541 ASN cc_start: 0.8883 (m-40) cc_final: 0.8385 (m110) REVERT: E 205 PHE cc_start: 0.8380 (t80) cc_final: 0.7963 (t80) REVERT: E 357 MET cc_start: 0.6916 (mmm) cc_final: 0.6585 (mmm) REVERT: F 205 PHE cc_start: 0.8404 (t80) cc_final: 0.7828 (t80) REVERT: F 422 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7315 (m-80) outliers start: 78 outliers final: 43 residues processed: 203 average time/residue: 0.3667 time to fit residues: 124.5158 Evaluate side-chains 156 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 108 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 572 ASN Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 236 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 307 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN B 723 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 231 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29360 Z= 0.208 Angle : 0.560 13.021 39664 Z= 0.289 Chirality : 0.043 0.604 4354 Planarity : 0.003 0.037 5106 Dihedral : 6.606 67.482 4210 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.29 % Allowed : 11.89 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3560 helix: 1.48 (0.13), residues: 1662 sheet: -0.71 (0.28), residues: 334 loop : -1.17 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 740 HIS 0.005 0.001 HIS B 475 PHE 0.016 0.001 PHE D 22 TYR 0.034 0.001 TYR E 218 ARG 0.003 0.000 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 116 time to evaluate : 3.153 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: A 432 MET cc_start: 0.8219 (mtp) cc_final: 0.7484 (ttm) REVERT: A 474 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8752 (pp) REVERT: A 635 MET cc_start: 0.9324 (mtm) cc_final: 0.9069 (mtm) REVERT: B 126 ASP cc_start: 0.7915 (t70) cc_final: 0.7542 (t0) REVERT: B 198 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8933 (p0) REVERT: B 364 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7765 (mpt180) REVERT: B 679 MET cc_start: 0.8831 (mtt) cc_final: 0.8514 (mtm) REVERT: C 62 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8481 (pp) REVERT: C 112 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8781 (tm) REVERT: C 309 MET cc_start: 0.8804 (ttm) cc_final: 0.8446 (mtp) REVERT: C 367 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8034 (mm-30) REVERT: C 499 MET cc_start: 0.8394 (ptm) cc_final: 0.7985 (ptm) REVERT: C 514 TYR cc_start: 0.8079 (m-10) cc_final: 0.7330 (m-80) REVERT: C 538 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8529 (m) REVERT: C 541 ASN cc_start: 0.8859 (m-40) cc_final: 0.8328 (m110) REVERT: D 62 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8613 (pp) REVERT: D 112 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8948 (tm) REVERT: D 309 MET cc_start: 0.8705 (ttm) cc_final: 0.8371 (mtp) REVERT: D 499 MET cc_start: 0.8460 (ptm) cc_final: 0.8082 (ptm) REVERT: D 514 TYR cc_start: 0.8051 (m-10) cc_final: 0.7330 (m-80) REVERT: D 538 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8543 (m) REVERT: D 541 ASN cc_start: 0.8820 (m-40) cc_final: 0.8330 (m110) REVERT: E 205 PHE cc_start: 0.8268 (t80) cc_final: 0.7665 (t80) REVERT: E 263 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: E 346 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8114 (pp30) REVERT: E 357 MET cc_start: 0.6909 (mmm) cc_final: 0.6697 (mmm) REVERT: F 205 PHE cc_start: 0.8127 (t80) cc_final: 0.7495 (t80) REVERT: F 352 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8950 (mt) REVERT: F 422 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7162 (m-80) outliers start: 103 outliers final: 56 residues processed: 209 average time/residue: 0.3427 time to fit residues: 121.4457 Evaluate side-chains 173 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 105 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 200 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 342 optimal weight: 0.0060 chunk 284 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 475 HIS B 640 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 29360 Z= 0.147 Angle : 0.539 17.160 39664 Z= 0.276 Chirality : 0.043 0.740 4354 Planarity : 0.003 0.041 5106 Dihedral : 6.294 65.191 4210 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.72 % Allowed : 12.53 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3560 helix: 1.81 (0.13), residues: 1640 sheet: -0.57 (0.28), residues: 334 loop : -1.14 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 PHE 0.014 0.001 PHE C 22 TYR 0.028 0.001 TYR F 422 ARG 0.004 0.000 ARG F 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 132 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8059 (mtp) cc_final: 0.7479 (ttm) REVERT: A 635 MET cc_start: 0.9296 (mtm) cc_final: 0.9071 (mtm) REVERT: B 126 ASP cc_start: 0.7802 (t70) cc_final: 0.7432 (t0) REVERT: C 62 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8603 (pp) REVERT: C 112 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8753 (tm) REVERT: C 309 MET cc_start: 0.8658 (ttm) cc_final: 0.8369 (mtp) REVERT: C 367 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8015 (mm-30) REVERT: C 499 MET cc_start: 0.8399 (ptm) cc_final: 0.8018 (ptm) REVERT: C 514 TYR cc_start: 0.8082 (m-10) cc_final: 0.7351 (m-80) REVERT: C 541 ASN cc_start: 0.8738 (m-40) cc_final: 0.8228 (m110) REVERT: D 62 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8457 (pp) REVERT: D 112 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8922 (tm) REVERT: D 309 MET cc_start: 0.8607 (ttm) cc_final: 0.8248 (mtp) REVERT: D 499 MET cc_start: 0.8420 (ptm) cc_final: 0.7980 (ptm) REVERT: D 514 TYR cc_start: 0.8045 (m-10) cc_final: 0.7354 (m-80) REVERT: D 541 ASN cc_start: 0.8755 (m-40) cc_final: 0.8255 (m110) REVERT: E 205 PHE cc_start: 0.8244 (t80) cc_final: 0.7755 (t80) REVERT: E 263 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: E 357 MET cc_start: 0.6826 (mmm) cc_final: 0.6564 (mmm) REVERT: F 205 PHE cc_start: 0.8119 (t80) cc_final: 0.7450 (t80) REVERT: F 422 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7215 (m-80) outliers start: 85 outliers final: 58 residues processed: 210 average time/residue: 0.3519 time to fit residues: 127.2454 Evaluate side-chains 176 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 112 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 341 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 379 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29360 Z= 0.336 Angle : 0.612 11.071 39664 Z= 0.315 Chirality : 0.046 0.552 4354 Planarity : 0.004 0.043 5106 Dihedral : 6.379 65.228 4210 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.42 % Allowed : 12.63 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3560 helix: 1.70 (0.13), residues: 1656 sheet: -0.79 (0.27), residues: 362 loop : -1.12 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.006 0.001 HIS A 699 PHE 0.022 0.002 PHE A 442 TYR 0.020 0.002 TYR F 422 ARG 0.005 0.001 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 109 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8260 (mtp) cc_final: 0.7617 (ttm) REVERT: A 474 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8803 (pp) REVERT: A 635 MET cc_start: 0.9373 (mtm) cc_final: 0.9102 (mtm) REVERT: B 126 ASP cc_start: 0.8167 (t70) cc_final: 0.7760 (t0) REVERT: B 198 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8946 (p0) REVERT: B 364 ARG cc_start: 0.8353 (mpt180) cc_final: 0.7978 (mmt-90) REVERT: B 474 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8773 (pp) REVERT: B 679 MET cc_start: 0.8835 (mtt) cc_final: 0.8514 (mtm) REVERT: C 62 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8686 (pp) REVERT: C 112 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8808 (tm) REVERT: C 309 MET cc_start: 0.8662 (ttm) cc_final: 0.8389 (mtp) REVERT: C 499 MET cc_start: 0.8499 (ptm) cc_final: 0.8088 (ptm) REVERT: C 514 TYR cc_start: 0.8131 (m-10) cc_final: 0.7395 (m-80) REVERT: C 538 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8535 (p) REVERT: C 541 ASN cc_start: 0.8770 (m-40) cc_final: 0.8296 (m110) REVERT: D 62 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8699 (pp) REVERT: D 112 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8909 (tm) REVERT: D 309 MET cc_start: 0.8619 (ttm) cc_final: 0.8330 (mtp) REVERT: D 499 MET cc_start: 0.8554 (ptm) cc_final: 0.8292 (ptm) REVERT: D 514 TYR cc_start: 0.8028 (m-10) cc_final: 0.7517 (m-80) REVERT: D 538 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8599 (m) REVERT: D 541 ASN cc_start: 0.8813 (m-40) cc_final: 0.8314 (m110) REVERT: E 205 PHE cc_start: 0.8188 (t80) cc_final: 0.7748 (t80) REVERT: E 263 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: E 352 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8942 (mt) REVERT: E 357 MET cc_start: 0.7053 (mmm) cc_final: 0.6770 (mmm) REVERT: F 205 PHE cc_start: 0.8075 (t80) cc_final: 0.7482 (t80) REVERT: F 263 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: F 325 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8596 (pt) REVERT: F 352 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8937 (mt) REVERT: F 422 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7152 (m-80) outliers start: 107 outliers final: 71 residues processed: 208 average time/residue: 0.3575 time to fit residues: 127.1847 Evaluate side-chains 184 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 98 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 684 HIS B 684 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 29360 Z= 0.146 Angle : 0.546 18.663 39664 Z= 0.279 Chirality : 0.042 0.491 4354 Planarity : 0.003 0.045 5106 Dihedral : 6.190 63.338 4210 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.59 % Allowed : 13.43 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3560 helix: 1.90 (0.13), residues: 1660 sheet: -0.66 (0.27), residues: 354 loop : -1.02 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 740 HIS 0.004 0.001 HIS C 249 PHE 0.016 0.001 PHE E 205 TYR 0.023 0.001 TYR F 422 ARG 0.003 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 107 time to evaluate : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.7979 (mtp) cc_final: 0.7554 (ttm) REVERT: A 474 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8776 (pp) REVERT: B 126 ASP cc_start: 0.7937 (t70) cc_final: 0.7584 (t0) REVERT: B 364 ARG cc_start: 0.7784 (mpt180) cc_final: 0.7275 (mmt-90) REVERT: B 474 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8635 (pp) REVERT: C 62 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8570 (pp) REVERT: C 112 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8783 (tm) REVERT: C 309 MET cc_start: 0.8637 (ttm) cc_final: 0.8356 (mtp) REVERT: C 499 MET cc_start: 0.8506 (ptm) cc_final: 0.8086 (ptm) REVERT: C 514 TYR cc_start: 0.8071 (m-10) cc_final: 0.7295 (m-80) REVERT: C 538 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 541 ASN cc_start: 0.8745 (m-40) cc_final: 0.8229 (m110) REVERT: D 62 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8478 (pp) REVERT: D 112 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8925 (tm) REVERT: D 309 MET cc_start: 0.8646 (ttm) cc_final: 0.8358 (mtp) REVERT: D 499 MET cc_start: 0.8566 (ptm) cc_final: 0.8106 (ptm) REVERT: D 514 TYR cc_start: 0.8124 (m-10) cc_final: 0.7379 (m-80) REVERT: D 538 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8514 (p) REVERT: D 541 ASN cc_start: 0.8767 (m-40) cc_final: 0.8264 (m110) REVERT: E 205 PHE cc_start: 0.8354 (t80) cc_final: 0.7802 (t80) REVERT: E 263 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: E 346 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7987 (pp30) REVERT: E 352 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8892 (mt) REVERT: E 357 MET cc_start: 0.6884 (mmm) cc_final: 0.6615 (mmm) REVERT: F 205 PHE cc_start: 0.8053 (t80) cc_final: 0.7444 (t80) REVERT: F 263 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: F 325 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8440 (pt) REVERT: F 422 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7150 (m-80) outliers start: 81 outliers final: 58 residues processed: 182 average time/residue: 0.3488 time to fit residues: 108.9863 Evaluate side-chains 175 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 103 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 7.9990 chunk 326 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 317 optimal weight: 0.0980 chunk 191 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 249 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 287 optimal weight: 9.9990 chunk 300 optimal weight: 0.9990 chunk 316 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29360 Z= 0.212 Angle : 0.552 17.720 39664 Z= 0.283 Chirality : 0.043 0.447 4354 Planarity : 0.003 0.045 5106 Dihedral : 6.093 62.224 4210 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.97 % Allowed : 13.04 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3560 helix: 1.93 (0.13), residues: 1658 sheet: -0.64 (0.27), residues: 354 loop : -1.00 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 740 HIS 0.005 0.001 HIS C 249 PHE 0.017 0.001 PHE D 22 TYR 0.025 0.001 TYR F 525 ARG 0.003 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 106 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8056 (mtp) cc_final: 0.7584 (ttm) REVERT: A 474 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8737 (pp) REVERT: B 126 ASP cc_start: 0.8011 (t70) cc_final: 0.7655 (t0) REVERT: B 152 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: B 364 ARG cc_start: 0.7537 (mpt180) cc_final: 0.7268 (mmt180) REVERT: B 474 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8694 (pp) REVERT: B 679 MET cc_start: 0.8879 (mtt) cc_final: 0.8561 (mtm) REVERT: C 62 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8578 (pp) REVERT: C 112 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8795 (tm) REVERT: C 309 MET cc_start: 0.8590 (ttm) cc_final: 0.8284 (mtp) REVERT: C 499 MET cc_start: 0.8505 (ptm) cc_final: 0.8111 (ptm) REVERT: C 514 TYR cc_start: 0.8107 (m-10) cc_final: 0.7313 (m-80) REVERT: C 538 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8505 (p) REVERT: C 541 ASN cc_start: 0.8761 (m-40) cc_final: 0.8237 (m110) REVERT: D 62 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8526 (pp) REVERT: D 112 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8935 (tm) REVERT: D 309 MET cc_start: 0.8584 (ttm) cc_final: 0.8314 (mtp) REVERT: D 499 MET cc_start: 0.8595 (ptm) cc_final: 0.8148 (ptm) REVERT: D 514 TYR cc_start: 0.8152 (m-10) cc_final: 0.7390 (m-80) REVERT: D 538 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8533 (p) REVERT: D 541 ASN cc_start: 0.8781 (m-40) cc_final: 0.8272 (m110) REVERT: E 205 PHE cc_start: 0.8336 (t80) cc_final: 0.7786 (t80) REVERT: E 263 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: E 352 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8943 (mt) REVERT: E 357 MET cc_start: 0.6935 (mmm) cc_final: 0.6652 (mmm) REVERT: F 205 PHE cc_start: 0.8120 (t80) cc_final: 0.7488 (t80) REVERT: F 263 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: F 325 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8450 (pt) REVERT: F 422 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7085 (m-80) outliers start: 93 outliers final: 65 residues processed: 193 average time/residue: 0.3703 time to fit residues: 121.3974 Evaluate side-chains 182 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 103 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 352 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 280 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 172 optimal weight: 30.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29360 Z= 0.222 Angle : 0.556 17.123 39664 Z= 0.285 Chirality : 0.043 0.431 4354 Planarity : 0.003 0.046 5106 Dihedral : 6.049 61.456 4210 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.85 % Allowed : 13.24 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3560 helix: 1.94 (0.13), residues: 1660 sheet: -0.61 (0.27), residues: 358 loop : -0.99 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 740 HIS 0.005 0.001 HIS C 249 PHE 0.017 0.001 PHE D 22 TYR 0.025 0.001 TYR F 525 ARG 0.004 0.000 ARG F 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 105 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8068 (mtp) cc_final: 0.7593 (ttm) REVERT: A 474 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8735 (pp) REVERT: B 126 ASP cc_start: 0.8039 (t70) cc_final: 0.7673 (t0) REVERT: B 152 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: B 364 ARG cc_start: 0.7547 (mpt180) cc_final: 0.7035 (mmt180) REVERT: B 474 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8708 (pp) REVERT: C 62 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8499 (pp) REVERT: C 112 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8802 (tm) REVERT: C 309 MET cc_start: 0.8584 (ttm) cc_final: 0.8287 (mtp) REVERT: C 499 MET cc_start: 0.8547 (ptm) cc_final: 0.8141 (ptm) REVERT: C 514 TYR cc_start: 0.8135 (m-10) cc_final: 0.7306 (m-80) REVERT: C 538 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8564 (p) REVERT: C 541 ASN cc_start: 0.8763 (m-40) cc_final: 0.8236 (m110) REVERT: D 62 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8513 (pp) REVERT: D 112 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8929 (tm) REVERT: D 309 MET cc_start: 0.8700 (ttm) cc_final: 0.8377 (mtp) REVERT: D 313 MET cc_start: 0.9180 (tpp) cc_final: 0.8772 (mmm) REVERT: D 499 MET cc_start: 0.8526 (ptm) cc_final: 0.8102 (ptm) REVERT: D 514 TYR cc_start: 0.8149 (m-10) cc_final: 0.7523 (m-10) REVERT: D 538 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 541 ASN cc_start: 0.8789 (m-40) cc_final: 0.8274 (m110) REVERT: E 205 PHE cc_start: 0.8333 (t80) cc_final: 0.7781 (t80) REVERT: E 263 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: E 352 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8944 (mt) REVERT: E 357 MET cc_start: 0.6947 (mmm) cc_final: 0.6660 (mmm) REVERT: F 205 PHE cc_start: 0.8162 (t80) cc_final: 0.7481 (t80) REVERT: F 263 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: F 325 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8447 (pt) REVERT: F 422 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7038 (m-80) outliers start: 89 outliers final: 70 residues processed: 187 average time/residue: 0.3553 time to fit residues: 114.2648 Evaluate side-chains 184 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 100 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 20.0000 chunk 299 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 258 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 281 optimal weight: 0.0980 chunk 117 optimal weight: 0.9980 chunk 288 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089867 restraints weight = 54570.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.088160 restraints weight = 67532.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089360 restraints weight = 66714.373| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29360 Z= 0.135 Angle : 0.528 16.517 39664 Z= 0.268 Chirality : 0.041 0.420 4354 Planarity : 0.003 0.045 5106 Dihedral : 5.879 58.602 4210 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.46 % Allowed : 13.75 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3560 helix: 2.07 (0.13), residues: 1658 sheet: -0.53 (0.28), residues: 354 loop : -0.93 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 453 HIS 0.004 0.001 HIS C 249 PHE 0.015 0.001 PHE C 84 TYR 0.025 0.001 TYR F 525 ARG 0.005 0.000 ARG F 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4306.31 seconds wall clock time: 80 minutes 24.92 seconds (4824.92 seconds total)