Starting phenix.real_space_refine on Tue Mar 19 21:30:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/03_2024/7wv3_32844_updated.pdb" } resolution = 2.26 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= -0.018 sd= 0.985 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 158 5.49 5 S 72 5.16 5 C 15564 2.51 5 N 4236 2.21 5 O 5356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25386 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5354 Classifications: {'peptide': 668} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 641} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5354 Classifications: {'peptide': 668} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 641} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5354 Classifications: {'peptide': 668} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 641} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5354 Classifications: {'peptide': 668} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 641} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1597 Classifications: {'RNA': 80} Modifications used: {'5*END': 1, 'rna3p_pyr': 80} Link IDs: {'rna3p': 79} Chain: "F" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1757 Classifications: {'RNA': 80} Modifications used: {'5*END': 1, 'rna3p': 80} Link IDs: {'rna3p': 79} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 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: "M" 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: "N" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.55, per 1000 atoms: 0.53 Number of scatterers: 25386 At special positions: 0 Unit cell: (112.628, 110.972, 259.211, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 158 15.00 O 5356 8.00 N 4236 7.00 C 15564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.01 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 677 " distance=2.01 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 677 " distance=2.01 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 649 " - pdb=" SG CYS D 677 " distance=2.01 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1001 " - " ASN A 196 " " NAG A1002 " - " ASN A 247 " " NAG A1003 " - " ASN A 252 " " NAG A1004 " - " ASN A 265 " " NAG A1005 " - " ASN A 291 " " NAG A1006 " - " ASN A 398 " " NAG A1007 " - " ASN A 507 " " NAG B1001 " - " ASN B 196 " " NAG B1002 " - " ASN B 247 " " NAG B1003 " - " ASN B 252 " " NAG B1004 " - " ASN B 265 " " NAG B1005 " - " ASN B 291 " " NAG B1006 " - " ASN B 398 " " NAG B1007 " - " ASN B 507 " " NAG C1001 " - " ASN C 196 " " NAG C1002 " - " ASN C 247 " " NAG C1003 " - " ASN C 252 " " NAG C1004 " - " ASN C 265 " " NAG C1005 " - " ASN C 291 " " NAG C1006 " - " ASN C 398 " " NAG C1007 " - " ASN C 507 " " NAG D1001 " - " ASN D 196 " " NAG D1002 " - " ASN D 247 " " NAG D1003 " - " ASN D 252 " " NAG D1004 " - " ASN D 265 " " NAG D1005 " - " ASN D 291 " " NAG D1006 " - " ASN D 398 " " NAG D1007 " - " ASN D 507 " " NAG G 1 " - " ASN A 57 " " NAG H 1 " - " ASN A 413 " " NAG I 1 " - " ASN B 57 " " NAG J 1 " - " ASN B 413 " " NAG K 1 " - " ASN C 57 " " NAG L 1 " - " ASN C 413 " " NAG M 1 " - " ASN D 57 " " NAG N 1 " - " ASN D 413 " Time building additional restraints: 11.27 Conformation dependent library (CDL) restraints added in 3.9 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 12 sheets defined 7.8% alpha, 8.1% beta 0 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 11.12 Creating SS restraints... Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 671 through 674 No H-bonds generated for 'chain 'A' and resid 671 through 674' Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 627 through 630 No H-bonds generated for 'chain 'B' and resid 627 through 630' Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 671 through 674 No H-bonds generated for 'chain 'B' and resid 671 through 674' Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 270 through 273 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 627 through 630 No H-bonds generated for 'chain 'C' and resid 627 through 630' Processing helix chain 'C' and resid 655 through 662 Processing helix chain 'C' and resid 671 through 674 No H-bonds generated for 'chain 'C' and resid 671 through 674' Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 234 through 245 Processing helix chain 'D' and resid 270 through 273 Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 627 through 630 No H-bonds generated for 'chain 'D' and resid 627 through 630' Processing helix chain 'D' and resid 655 through 662 Processing helix chain 'D' and resid 671 through 674 No H-bonds generated for 'chain 'D' and resid 671 through 674' Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.299A pdb=" N VAL A 55 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER A 79 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 103 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A 127 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR A 151 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU A 175 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS A 201 " --> pdb=" O LEU A 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.438A pdb=" N ASN A 252 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET A 278 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR A 302 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR A 326 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS A 359 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR A 383 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A 411 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 435 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU A 460 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG A 484 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 510 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 534 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 566 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 590 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER A 614 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU A 639 " --> pdb=" O LEU A 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 444 through 446 removed outlier: 6.053A pdb=" N TYR A 468 " --> pdb=" O GLN A 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.299A pdb=" N VAL B 55 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER B 79 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 103 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B 127 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B 151 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU B 175 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.437A pdb=" N ASN B 252 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET B 278 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR B 302 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 326 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS B 359 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR B 383 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 411 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 435 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU B 460 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 534 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 566 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 590 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER B 614 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU B 639 " --> pdb=" O LEU B 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 444 through 446 removed outlier: 6.052A pdb=" N TYR B 468 " --> pdb=" O GLN B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 34 through 36 removed outlier: 6.300A pdb=" N VAL C 55 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER C 79 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C 103 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU C 127 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 151 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU C 175 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS C 201 " --> pdb=" O LEU C 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 225 through 227 removed outlier: 6.438A pdb=" N ASN C 252 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET C 278 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR C 302 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR C 326 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS C 359 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR C 383 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE C 411 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 435 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU C 460 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG C 484 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE C 510 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 534 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 566 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE C 590 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 614 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU C 639 " --> pdb=" O LEU C 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 444 through 446 removed outlier: 6.053A pdb=" N TYR C 468 " --> pdb=" O GLN C 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 34 through 36 removed outlier: 6.300A pdb=" N VAL D 55 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER D 79 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 103 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU D 127 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR D 151 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU D 175 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS D 201 " --> pdb=" O LEU D 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 225 through 227 removed outlier: 6.439A pdb=" N ASN D 252 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET D 278 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR D 302 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR D 326 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS D 359 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR D 383 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE D 411 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 435 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU D 460 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG D 484 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 510 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D 534 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 566 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE D 590 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER D 614 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU D 639 " --> pdb=" O LEU D 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 444 through 446 removed outlier: 6.053A pdb=" N TYR D 468 " --> pdb=" O GLN D 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 60 hydrogen bonds defined for protein. 144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 8.14 Time building geometry restraints manager: 11.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7030 1.33 - 1.45: 5172 1.45 - 1.57: 13614 1.57 - 1.69: 316 1.69 - 1.81: 104 Bond restraints: 26236 Sorted by residual: bond pdb=" C2 I F 23 " pdb=" N3 I F 23 " ideal model delta sigma weight residual 1.462 1.304 0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" C2 I F 57 " pdb=" N3 I F 57 " ideal model delta sigma weight residual 1.462 1.305 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C2 I F 60 " pdb=" N3 I F 60 " ideal model delta sigma weight residual 1.462 1.306 0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C2 I F 55 " pdb=" N3 I F 55 " ideal model delta sigma weight residual 1.462 1.307 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C2 I F 56 " pdb=" N3 I F 56 " ideal model delta sigma weight residual 1.462 1.307 0.155 2.00e-02 2.50e+03 5.99e+01 ... (remaining 26231 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.21: 1607 107.21 - 113.94: 15838 113.94 - 120.67: 9669 120.67 - 127.39: 8670 127.39 - 134.12: 564 Bond angle restraints: 36348 Sorted by residual: angle pdb=" C1' I F 43 " pdb=" N9 I F 43 " pdb=" C4 I F 43 " ideal model delta sigma weight residual 106.08 124.74 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C1' I F 64 " pdb=" N9 I F 64 " pdb=" C4 I F 64 " ideal model delta sigma weight residual 106.08 124.53 -18.45 3.00e+00 1.11e-01 3.78e+01 angle pdb=" C1' I F 53 " pdb=" N9 I F 53 " pdb=" C4 I F 53 " ideal model delta sigma weight residual 106.08 124.47 -18.39 3.00e+00 1.11e-01 3.76e+01 angle pdb=" C1' I F 39 " pdb=" N9 I F 39 " pdb=" C4 I F 39 " ideal model delta sigma weight residual 106.08 124.28 -18.20 3.00e+00 1.11e-01 3.68e+01 angle pdb=" C1' I F 21 " pdb=" N9 I F 21 " pdb=" C4 I F 21 " ideal model delta sigma weight residual 106.08 124.22 -18.14 3.00e+00 1.11e-01 3.66e+01 ... (remaining 36343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14816 18.05 - 36.10: 745 36.10 - 54.16: 319 54.16 - 72.21: 240 72.21 - 90.26: 248 Dihedral angle restraints: 16368 sinusoidal: 8508 harmonic: 7860 Sorted by residual: dihedral pdb=" CA SER C 498 " pdb=" C SER C 498 " pdb=" N PRO C 499 " pdb=" CA PRO C 499 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA SER B 498 " pdb=" C SER B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA SER A 498 " pdb=" C SER A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 16365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3844 0.101 - 0.202: 215 0.202 - 0.303: 8 0.303 - 0.404: 0 0.404 - 0.504: 4 Chirality restraints: 4071 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 57 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 4068 not shown) Planarity restraints: 4124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I F 20 " 0.212 2.00e-02 2.50e+03 6.13e-01 8.46e+03 pdb=" C2' I F 20 " -0.169 2.00e-02 2.50e+03 pdb=" C3' I F 20 " -0.602 2.00e-02 2.50e+03 pdb=" C4' I F 20 " 0.443 2.00e-02 2.50e+03 pdb=" C5' I F 20 " 0.075 2.00e-02 2.50e+03 pdb=" N9 I F 20 " -0.939 2.00e-02 2.50e+03 pdb=" O2' I F 20 " 1.007 2.00e-02 2.50e+03 pdb=" O3' I F 20 " -0.665 2.00e-02 2.50e+03 pdb=" O4' I F 20 " 0.639 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 24 " 0.214 2.00e-02 2.50e+03 6.08e-01 8.32e+03 pdb=" C2' I F 24 " -0.180 2.00e-02 2.50e+03 pdb=" C3' I F 24 " -0.600 2.00e-02 2.50e+03 pdb=" C4' I F 24 " 0.442 2.00e-02 2.50e+03 pdb=" C5' I F 24 " 0.058 2.00e-02 2.50e+03 pdb=" N9 I F 24 " -0.938 2.00e-02 2.50e+03 pdb=" O2' I F 24 " 0.978 2.00e-02 2.50e+03 pdb=" O3' I F 24 " -0.641 2.00e-02 2.50e+03 pdb=" O4' I F 24 " 0.666 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 58 " 0.211 2.00e-02 2.50e+03 6.07e-01 8.29e+03 pdb=" C2' I F 58 " -0.181 2.00e-02 2.50e+03 pdb=" C3' I F 58 " -0.597 2.00e-02 2.50e+03 pdb=" C4' I F 58 " 0.441 2.00e-02 2.50e+03 pdb=" C5' I F 58 " 0.058 2.00e-02 2.50e+03 pdb=" N9 I F 58 " -0.938 2.00e-02 2.50e+03 pdb=" O2' I F 58 " 0.976 2.00e-02 2.50e+03 pdb=" O3' I F 58 " -0.637 2.00e-02 2.50e+03 pdb=" O4' I F 58 " 0.667 2.00e-02 2.50e+03 ... (remaining 4121 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4997 2.77 - 3.30: 22836 3.30 - 3.84: 45203 3.84 - 4.37: 57623 4.37 - 4.90: 88540 Nonbonded interactions: 219199 Sorted by model distance: nonbonded pdb=" O THR A 391 " pdb=" NH2 ARG A 394 " model vdw 2.241 2.520 nonbonded pdb=" O THR D 391 " pdb=" NH2 ARG D 394 " model vdw 2.241 2.520 nonbonded pdb=" O THR B 391 " pdb=" NH2 ARG B 394 " model vdw 2.241 2.520 nonbonded pdb=" O THR C 391 " pdb=" NH2 ARG C 394 " model vdw 2.242 2.520 nonbonded pdb=" O MET B 362 " pdb=" OG SER B 389 " model vdw 2.268 2.440 ... (remaining 219194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 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: 24.140 Check model and map are aligned: 0.370 Set scattering table: 0.250 Process input model: 73.770 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.015 0.158 26236 Z= 0.941 Angle : 1.469 18.663 36348 Z= 0.545 Chirality : 0.053 0.504 4071 Planarity : 0.082 0.613 4088 Dihedral : 18.720 90.258 11200 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.32 % Allowed : 3.05 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2664 helix: -1.62 (0.37), residues: 196 sheet: -1.57 (0.27), residues: 420 loop : 0.23 (0.15), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 429 HIS 0.005 0.001 HIS B 359 PHE 0.011 0.002 PHE D 606 TYR 0.012 0.002 TYR A 462 ARG 0.004 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 317 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5957 (m-40) cc_final: 0.5539 (m-40) REVERT: A 85 ASN cc_start: 0.5462 (m-40) cc_final: 0.5256 (m-40) REVERT: A 100 MET cc_start: 0.2141 (mmt) cc_final: 0.1266 (tmm) REVERT: A 159 LEU cc_start: 0.8050 (mt) cc_final: 0.7821 (mt) REVERT: A 183 ILE cc_start: 0.7609 (mt) cc_final: 0.7348 (mp) REVERT: A 224 PHE cc_start: 0.7652 (m-10) cc_final: 0.7110 (m-80) REVERT: A 335 LYS cc_start: 0.6941 (mmtm) cc_final: 0.6477 (mmmt) REVERT: B 326 TYR cc_start: 0.7400 (t80) cc_final: 0.7061 (m-80) REVERT: C 137 LYS cc_start: 0.7823 (ptpp) cc_final: 0.7574 (ptmt) REVERT: C 682 HIS cc_start: 0.6034 (t-90) cc_final: 0.5822 (t70) outliers start: 8 outliers final: 2 residues processed: 323 average time/residue: 1.3808 time to fit residues: 514.5573 Evaluate side-chains 156 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain B residue 122 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 139 optimal weight: 0.0050 chunk 110 optimal weight: 0.5980 chunk 213 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 380 ASN A 474 ASN B 62 GLN B 133 ASN B 597 ASN B 667 ASN C 113 GLN C 257 ASN C 299 GLN C 457 ASN C 548 HIS C 597 ASN D 124 ASN D 141 ASN D 207 ASN D 548 HIS D 682 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26236 Z= 0.202 Angle : 1.960 18.635 36348 Z= 1.187 Chirality : 0.042 0.364 4071 Planarity : 0.015 0.128 4088 Dihedral : 21.215 95.461 5942 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.61 % Allowed : 8.28 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2664 helix: -0.82 (0.46), residues: 144 sheet: -1.59 (0.27), residues: 420 loop : 0.16 (0.15), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 660 HIS 0.011 0.001 HIS D 108 PHE 0.019 0.001 PHE D 84 TYR 0.007 0.001 TYR C 468 ARG 0.006 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5942 (m-40) cc_final: 0.5501 (m-40) REVERT: A 100 MET cc_start: 0.2182 (mmt) cc_final: 0.1294 (tmm) REVERT: A 106 LEU cc_start: 0.8297 (mt) cc_final: 0.8095 (mm) REVERT: A 125 LEU cc_start: 0.6724 (mt) cc_final: 0.6327 (mp) REVERT: A 133 ASN cc_start: 0.7619 (m-40) cc_final: 0.7314 (t0) REVERT: A 159 LEU cc_start: 0.8011 (mt) cc_final: 0.7775 (mt) REVERT: A 183 ILE cc_start: 0.7643 (mt) cc_final: 0.7377 (mp) REVERT: A 335 LYS cc_start: 0.6964 (mmtm) cc_final: 0.6470 (mmmt) REVERT: A 374 MET cc_start: 0.7062 (ttm) cc_final: 0.6725 (tpp) REVERT: B 64 ARG cc_start: 0.6075 (tpp80) cc_final: 0.5640 (tpp80) REVERT: B 326 TYR cc_start: 0.7423 (t80) cc_final: 0.7072 (m-80) REVERT: C 137 LYS cc_start: 0.7736 (ptpp) cc_final: 0.7530 (ptmt) REVERT: C 204 LEU cc_start: 0.8382 (mt) cc_final: 0.8139 (mm) REVERT: C 243 LEU cc_start: 0.8097 (tp) cc_final: 0.7806 (tm) REVERT: D 147 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6686 (mtmt) REVERT: D 456 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7331 (mm-30) outliers start: 40 outliers final: 14 residues processed: 194 average time/residue: 1.3196 time to fit residues: 299.3584 Evaluate side-chains 157 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 456 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 267 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN B 167 GLN B 380 ASN B 608 ASN C 62 GLN C 109 ASN C 257 ASN C 548 HIS D 124 ASN D 141 ASN D 218 HIS D 299 GLN D 359 HIS D 445 GLN D 548 HIS D 667 ASN D 682 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26236 Z= 0.318 Angle : 1.794 16.769 36348 Z= 1.095 Chirality : 0.047 0.537 4071 Planarity : 0.017 0.129 4088 Dihedral : 21.901 96.507 5942 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.41 % Allowed : 9.24 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2664 helix: -1.26 (0.39), residues: 176 sheet: -1.79 (0.26), residues: 416 loop : -0.06 (0.15), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 296 HIS 0.009 0.001 HIS D 682 PHE 0.012 0.002 PHE B 333 TYR 0.015 0.002 TYR B 683 ARG 0.004 0.001 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 158 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5697 (m-40) cc_final: 0.5249 (m-40) REVERT: A 100 MET cc_start: 0.2306 (mmt) cc_final: 0.1170 (tmm) REVERT: A 106 LEU cc_start: 0.8281 (mt) cc_final: 0.8078 (mm) REVERT: A 133 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7049 (t0) REVERT: A 183 ILE cc_start: 0.7545 (mt) cc_final: 0.7141 (mp) REVERT: A 209 ILE cc_start: 0.7254 (mm) cc_final: 0.6974 (mm) REVERT: A 224 PHE cc_start: 0.7638 (m-10) cc_final: 0.7114 (m-80) REVERT: A 335 LYS cc_start: 0.7015 (mmtm) cc_final: 0.6759 (mptt) REVERT: A 399 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7151 (mm-30) REVERT: A 503 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: B 653 SER cc_start: 0.7774 (OUTLIER) cc_final: 0.7540 (t) REVERT: B 689 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7276 (ptm160) REVERT: C 137 LYS cc_start: 0.7748 (ptpp) cc_final: 0.7507 (ptmt) REVERT: C 626 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: D 113 GLN cc_start: 0.7166 (tp40) cc_final: 0.6820 (mp10) REVERT: D 456 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7283 (mm-30) outliers start: 60 outliers final: 19 residues processed: 206 average time/residue: 1.2366 time to fit residues: 299.6154 Evaluate side-chains 168 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 650 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 235 optimal weight: 0.0770 chunk 70 optimal weight: 10.0000 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 287 ASN A 682 HIS C 109 ASN C 257 ASN C 548 HIS D 62 GLN D 124 ASN D 141 ASN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 GLN D 548 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26236 Z= 0.280 Angle : 1.737 16.563 36348 Z= 1.080 Chirality : 0.046 0.485 4071 Planarity : 0.016 0.128 4088 Dihedral : 21.878 98.202 5942 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.61 % Allowed : 10.61 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2664 helix: -1.56 (0.37), residues: 200 sheet: -1.92 (0.26), residues: 420 loop : -0.17 (0.15), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 660 HIS 0.010 0.001 HIS D 682 PHE 0.011 0.002 PHE D 557 TYR 0.017 0.002 TYR B 683 ARG 0.005 0.001 ARG C 635 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 158 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5682 (m-40) cc_final: 0.5206 (m-40) REVERT: A 100 MET cc_start: 0.2463 (mmt) cc_final: 0.1260 (tmm) REVERT: A 103 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6838 (m) REVERT: A 106 LEU cc_start: 0.8311 (mt) cc_final: 0.7981 (mm) REVERT: A 183 ILE cc_start: 0.7512 (mt) cc_final: 0.7252 (mt) REVERT: A 209 ILE cc_start: 0.7139 (mm) cc_final: 0.6867 (mm) REVERT: A 335 LYS cc_start: 0.7124 (mmtm) cc_final: 0.6741 (mmtt) REVERT: A 399 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 503 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: B 689 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7166 (ptm160) REVERT: C 137 LYS cc_start: 0.7858 (ptpp) cc_final: 0.7606 (ptmt) REVERT: C 626 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: D 456 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7340 (mm-30) outliers start: 65 outliers final: 28 residues processed: 206 average time/residue: 1.1759 time to fit residues: 288.0837 Evaluate side-chains 172 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 650 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 3 optimal weight: 0.0670 chunk 195 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 224 optimal weight: 0.4980 chunk 181 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 287 ASN A 682 HIS C 109 ASN C 257 ASN C 445 GLN C 457 ASN C 548 HIS D 124 ASN D 141 ASN D 548 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26236 Z= 0.249 Angle : 1.713 15.764 36348 Z= 1.070 Chirality : 0.045 0.472 4071 Planarity : 0.016 0.127 4088 Dihedral : 21.958 99.136 5942 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.29 % Allowed : 11.86 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2664 helix: -1.98 (0.33), residues: 224 sheet: -1.96 (0.26), residues: 420 loop : -0.22 (0.15), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 660 HIS 0.009 0.001 HIS D 682 PHE 0.010 0.001 PHE B 333 TYR 0.011 0.001 TYR A 383 ARG 0.003 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 145 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5765 (m-40) cc_final: 0.5322 (m-40) REVERT: A 100 MET cc_start: 0.2446 (mmt) cc_final: 0.1352 (tmm) REVERT: A 106 LEU cc_start: 0.8289 (mt) cc_final: 0.8049 (mm) REVERT: A 183 ILE cc_start: 0.7479 (mt) cc_final: 0.7216 (mt) REVERT: A 209 ILE cc_start: 0.7167 (mm) cc_final: 0.6884 (mm) REVERT: A 335 LYS cc_start: 0.7202 (mmtm) cc_final: 0.6811 (mmpt) REVERT: A 399 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 503 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: A 692 ASP cc_start: 0.6409 (p0) cc_final: 0.5443 (t0) REVERT: B 64 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5656 (tpp80) REVERT: B 689 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7162 (ptm160) REVERT: C 137 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7618 (ptmt) REVERT: C 204 LEU cc_start: 0.8380 (mt) cc_final: 0.8091 (mm) REVERT: C 222 ARG cc_start: 0.7075 (ptp90) cc_final: 0.6803 (mtm-85) REVERT: C 626 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: C 652 GLU cc_start: 0.7440 (pt0) cc_final: 0.7195 (pt0) REVERT: D 456 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7322 (mm-30) outliers start: 57 outliers final: 27 residues processed: 188 average time/residue: 1.1933 time to fit residues: 265.5276 Evaluate side-chains 174 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 575 ASP Chi-restraints excluded: chain D residue 650 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 64 optimal weight: 0.0570 chunk 263 optimal weight: 0.0030 chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 682 HIS C 109 ASN C 257 ASN C 457 ASN C 548 HIS D 141 ASN D 548 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26236 Z= 0.213 Angle : 1.685 15.268 36348 Z= 1.062 Chirality : 0.044 0.711 4071 Planarity : 0.016 0.125 4088 Dihedral : 22.012 100.923 5942 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.77 % Allowed : 11.66 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2664 helix: -1.91 (0.33), residues: 224 sheet: -1.93 (0.26), residues: 420 loop : -0.22 (0.15), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 660 HIS 0.010 0.001 HIS D 682 PHE 0.008 0.001 PHE D 557 TYR 0.010 0.001 TYR A 383 ARG 0.004 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 144 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5836 (m-40) cc_final: 0.5415 (m-40) REVERT: A 100 MET cc_start: 0.2375 (mmt) cc_final: 0.1468 (tmm) REVERT: A 106 LEU cc_start: 0.8312 (mt) cc_final: 0.8068 (mm) REVERT: A 335 LYS cc_start: 0.7151 (mmtm) cc_final: 0.6772 (mmpt) REVERT: A 399 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 503 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: B 64 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5672 (tpp80) REVERT: B 87 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7564 (mp) REVERT: B 163 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7489 (mmmm) REVERT: B 689 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7116 (ptm160) REVERT: C 137 LYS cc_start: 0.7846 (ptpp) cc_final: 0.7617 (ptmt) REVERT: C 204 LEU cc_start: 0.8404 (mt) cc_final: 0.8114 (mm) REVERT: C 243 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7554 (tm) REVERT: C 278 MET cc_start: 0.7830 (tmm) cc_final: 0.7596 (tmt) REVERT: C 626 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: C 652 GLU cc_start: 0.7419 (pt0) cc_final: 0.7156 (pt0) REVERT: D 456 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7311 (mm-30) outliers start: 69 outliers final: 27 residues processed: 195 average time/residue: 1.2098 time to fit residues: 278.8459 Evaluate side-chains 176 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 575 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 149 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 262 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 287 ASN A 608 ASN A 682 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN C 457 ASN C 548 HIS D 39 HIS D 141 ASN D 548 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 26236 Z= 0.445 Angle : 1.755 16.043 36348 Z= 1.076 Chirality : 0.054 0.876 4071 Planarity : 0.017 0.136 4088 Dihedral : 22.006 102.940 5942 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.73 % Allowed : 12.22 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2664 helix: -2.20 (0.32), residues: 224 sheet: -2.14 (0.26), residues: 420 loop : -0.45 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 296 HIS 0.008 0.001 HIS D 682 PHE 0.017 0.002 PHE D 557 TYR 0.016 0.002 TYR A 383 ARG 0.005 0.001 ARG D 484 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 148 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6943 (tp) REVERT: A 61 ASN cc_start: 0.5967 (m-40) cc_final: 0.5337 (m-40) REVERT: A 85 ASN cc_start: 0.5676 (m-40) cc_final: 0.5395 (m110) REVERT: A 86 THR cc_start: 0.6999 (OUTLIER) cc_final: 0.6748 (t) REVERT: A 100 MET cc_start: 0.2257 (mmt) cc_final: 0.2024 (mtp) REVERT: A 103 VAL cc_start: 0.7257 (OUTLIER) cc_final: 0.6934 (m) REVERT: A 106 LEU cc_start: 0.8356 (mt) cc_final: 0.8102 (mm) REVERT: A 259 GLN cc_start: 0.6771 (tp40) cc_final: 0.6372 (mp10) REVERT: A 335 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6841 (mmtt) REVERT: A 399 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 503 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: B 53 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5899 (pt) REVERT: B 64 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5710 (tpp80) REVERT: C 137 LYS cc_start: 0.7981 (ptpp) cc_final: 0.7586 (pttt) REVERT: C 243 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7529 (tm) REVERT: C 626 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: D 147 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7071 (mtmt) REVERT: D 171 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7306 (mp0) REVERT: D 456 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: D 663 GLU cc_start: 0.6827 (pp20) cc_final: 0.6467 (pp20) outliers start: 68 outliers final: 30 residues processed: 198 average time/residue: 1.1830 time to fit residues: 277.2951 Evaluate side-chains 181 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 575 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 156 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 682 HIS C 257 ASN C 285 ASN C 457 ASN C 548 HIS D 141 ASN D 457 ASN D 548 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26236 Z= 0.202 Angle : 1.682 15.292 36348 Z= 1.061 Chirality : 0.044 0.533 4071 Planarity : 0.016 0.124 4088 Dihedral : 21.963 103.702 5942 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.17 % Allowed : 12.94 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2664 helix: -1.88 (0.34), residues: 216 sheet: -2.01 (0.26), residues: 420 loop : -0.35 (0.15), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 273 HIS 0.012 0.001 HIS D 682 PHE 0.012 0.001 PHE B 333 TYR 0.011 0.001 TYR A 383 ARG 0.004 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 143 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6793 (tp) REVERT: A 61 ASN cc_start: 0.5932 (m-40) cc_final: 0.5341 (m-40) REVERT: A 100 MET cc_start: 0.2231 (mmt) cc_final: 0.2026 (mtp) REVERT: A 106 LEU cc_start: 0.8362 (mt) cc_final: 0.8156 (mm) REVERT: A 335 LYS cc_start: 0.7213 (mmtm) cc_final: 0.6688 (mmmt) REVERT: A 374 MET cc_start: 0.7245 (ttm) cc_final: 0.6589 (tpp) REVERT: A 399 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 503 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: B 64 ARG cc_start: 0.6328 (OUTLIER) cc_final: 0.5733 (tpp80) REVERT: C 137 LYS cc_start: 0.7927 (ptpp) cc_final: 0.7546 (pttt) REVERT: C 204 LEU cc_start: 0.8395 (mt) cc_final: 0.8114 (mm) REVERT: C 243 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7461 (tm) REVERT: C 278 MET cc_start: 0.7843 (tmm) cc_final: 0.7595 (tmt) REVERT: C 626 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: D 147 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6983 (mtmt) REVERT: D 167 GLN cc_start: 0.7468 (pt0) cc_final: 0.7135 (pt0) REVERT: D 456 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: D 530 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6806 (mm-30) outliers start: 54 outliers final: 30 residues processed: 177 average time/residue: 1.1804 time to fit residues: 248.6999 Evaluate side-chains 180 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 575 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS B 599 ASN C 109 ASN C 257 ASN C 285 ASN C 457 ASN C 548 HIS D 124 ASN D 141 ASN D 548 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26236 Z= 0.266 Angle : 1.687 15.237 36348 Z= 1.059 Chirality : 0.045 0.501 4071 Planarity : 0.017 0.129 4088 Dihedral : 22.063 104.775 5942 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.33 % Allowed : 12.90 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2664 helix: -2.03 (0.33), residues: 224 sheet: -2.04 (0.26), residues: 420 loop : -0.35 (0.15), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 273 HIS 0.009 0.001 HIS A 682 PHE 0.012 0.001 PHE B 333 TYR 0.011 0.001 TYR A 383 ARG 0.004 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 143 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6859 (tp) REVERT: A 61 ASN cc_start: 0.6055 (m-40) cc_final: 0.5421 (m-40) REVERT: A 85 ASN cc_start: 0.5703 (m-40) cc_final: 0.5375 (m110) REVERT: A 86 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6910 (t) REVERT: A 103 VAL cc_start: 0.7184 (t) cc_final: 0.6851 (m) REVERT: A 106 LEU cc_start: 0.8369 (mt) cc_final: 0.8156 (mm) REVERT: A 259 GLN cc_start: 0.6760 (tp40) cc_final: 0.6382 (mp10) REVERT: A 335 LYS cc_start: 0.7230 (mmtm) cc_final: 0.6831 (mmpt) REVERT: A 399 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 503 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: B 64 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.5746 (tpp80) REVERT: B 169 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: C 137 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7542 (pttt) REVERT: C 204 LEU cc_start: 0.8408 (mt) cc_final: 0.8111 (mm) REVERT: C 243 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7456 (tm) REVERT: C 278 MET cc_start: 0.7845 (tmm) cc_final: 0.7593 (tmt) REVERT: C 626 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7035 (mt-10) REVERT: D 147 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.7018 (mtmt) REVERT: D 167 GLN cc_start: 0.7517 (pt0) cc_final: 0.7162 (pt0) REVERT: D 456 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: D 530 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6866 (mm-30) outliers start: 58 outliers final: 31 residues processed: 185 average time/residue: 1.2098 time to fit residues: 263.6429 Evaluate side-chains 181 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 380 ASN Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 575 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 179 optimal weight: 0.3980 chunk 270 optimal weight: 6.9990 chunk 249 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 682 HIS C 109 ASN C 257 ASN C 285 ASN C 457 ASN C 548 HIS D 141 ASN D 548 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26236 Z= 0.195 Angle : 1.655 15.107 36348 Z= 1.053 Chirality : 0.043 0.401 4071 Planarity : 0.016 0.124 4088 Dihedral : 22.085 105.219 5942 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.05 % Allowed : 13.30 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2664 helix: -1.80 (0.34), residues: 216 sheet: -1.94 (0.26), residues: 420 loop : -0.32 (0.15), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 273 HIS 0.011 0.001 HIS D 682 PHE 0.010 0.001 PHE B 333 TYR 0.009 0.001 TYR A 383 ARG 0.004 0.000 ARG B 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 142 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6813 (tp) REVERT: A 61 ASN cc_start: 0.6087 (m-40) cc_final: 0.5468 (m-40) REVERT: A 85 ASN cc_start: 0.5483 (m-40) cc_final: 0.5129 (m110) REVERT: A 86 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.6996 (t) REVERT: A 106 LEU cc_start: 0.8286 (mt) cc_final: 0.8077 (mm) REVERT: A 335 LYS cc_start: 0.7234 (mmtm) cc_final: 0.6823 (mmpt) REVERT: A 399 GLU cc_start: 0.7266 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 503 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: B 64 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5776 (tpp80) REVERT: B 169 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: C 137 LYS cc_start: 0.7908 (ptpp) cc_final: 0.7511 (pttt) REVERT: C 204 LEU cc_start: 0.8412 (mt) cc_final: 0.8122 (mm) REVERT: C 243 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7440 (tm) REVERT: C 278 MET cc_start: 0.7818 (tmm) cc_final: 0.7581 (tmt) REVERT: C 626 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: D 147 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6997 (mtmt) REVERT: D 167 GLN cc_start: 0.7451 (pt0) cc_final: 0.7127 (pt0) REVERT: D 456 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: D 530 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6801 (mm-30) outliers start: 51 outliers final: 31 residues processed: 177 average time/residue: 1.1751 time to fit residues: 247.3792 Evaluate side-chains 180 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 380 ASN Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 575 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.4980 chunk 229 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 287 ASN A 682 HIS C 109 ASN C 257 ASN C 285 ASN C 457 ASN C 548 HIS D 133 ASN D 141 ASN D 548 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.169453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129322 restraints weight = 31187.929| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.81 r_work: 0.3557 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26236 Z= 0.225 Angle : 1.660 15.003 36348 Z= 1.053 Chirality : 0.044 0.403 4071 Planarity : 0.016 0.126 4088 Dihedral : 22.119 105.473 5942 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.93 % Allowed : 13.59 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2664 helix: -1.82 (0.34), residues: 216 sheet: -1.99 (0.26), residues: 420 loop : -0.33 (0.15), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 273 HIS 0.011 0.001 HIS A 682 PHE 0.011 0.001 PHE B 333 TYR 0.010 0.001 TYR A 383 ARG 0.004 0.000 ARG B 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8093.05 seconds wall clock time: 146 minutes 45.38 seconds (8805.38 seconds total)