Starting phenix.real_space_refine (version: dev) on Sat Feb 25 12:54:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/02_2023/7wv3_32844_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/02_2023/7wv3_32844.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/02_2023/7wv3_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_32844/02_2023/7wv3_32844_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/02_2023/7wv3_32844_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/02_2023/7wv3_32844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/02_2023/7wv3_32844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/02_2023/7wv3_32844_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv3_32844/02_2023/7wv3_32844_updated.pdb" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.018 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 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-4877/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 7 Time building chain proxies: 14.29, per 1000 atoms: 0.56 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: 11.34 Conformation dependent library (CDL) restraints added in 3.1 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: 9.51 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: 9.42 Time building geometry restraints manager: 11.89 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: 14131 18.05 - 36.10: 677 36.10 - 54.16: 184 54.16 - 72.21: 229 72.21 - 90.26: 169 Dihedral angle restraints: 15390 sinusoidal: 7530 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 15387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3856 0.101 - 0.202: 203 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 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. 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: 6.450 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: 25.190 Check model and map are aligned: 0.360 Process input model: 71.230 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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= 0.937 Angle : 1.456 18.663 36348 Z= 0.543 Chirality : 0.052 0.504 4071 Planarity : 0.082 0.613 4088 Dihedral : 17.577 90.258 10222 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 % 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 *********************** 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 : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 323 average time/residue: 1.4697 time to fit residues: 548.1274 Evaluate side-chains 155 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 2.847 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 3.8214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 61 ASN 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 26236 Z= 0.233 Angle : 1.953 18.716 36348 Z= 1.178 Chirality : 0.042 0.367 4071 Planarity : 0.015 0.126 4088 Dihedral : 20.351 97.580 4962 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.69 % 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: -1.60 (0.27), residues: 420 loop : 0.16 (0.15), residues: 2100 *********************** 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 207 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 14 residues processed: 194 average time/residue: 1.3682 time to fit residues: 309.8895 Evaluate side-chains 155 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 2.997 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.7120 time to fit residues: 6.6275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 247 optimal weight: 0.6980 chunk 267 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 245 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 133 ASN A 682 HIS B 133 ASN B 167 GLN B 169 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 682 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 26236 Z= 0.298 Angle : 1.785 16.007 36348 Z= 1.089 Chirality : 0.046 0.359 4071 Planarity : 0.017 0.131 4088 Dihedral : 21.203 96.192 4962 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 2.65 % 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: -0.80 (0.17), residues: 2664 helix: -1.30 (0.39), residues: 176 sheet: -1.89 (0.27), residues: 376 loop : -0.16 (0.14), residues: 2112 *********************** 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 222 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 156 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 18 residues processed: 210 average time/residue: 1.3323 time to fit residues: 329.3496 Evaluate side-chains 157 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.2870 time to fit residues: 5.9176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 128 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 167 GLN A 608 ASN A 682 HIS C 109 ASN C 257 ASN C 548 HIS D 62 GLN D 124 ASN D 141 ASN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 26236 Z= 0.372 Angle : 1.765 16.343 36348 Z= 1.088 Chirality : 0.049 0.494 4071 Planarity : 0.017 0.133 4088 Dihedral : 20.973 98.133 4962 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 2.69 % 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: -1.01 (0.17), residues: 2664 helix: -1.46 (0.38), residues: 176 sheet: -2.01 (0.26), residues: 420 loop : -0.26 (0.14), residues: 2068 *********************** 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 224 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 157 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 33 residues processed: 205 average time/residue: 1.2348 time to fit residues: 300.3476 Evaluate side-chains 171 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 2.724 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 9 average time/residue: 0.5219 time to fit residues: 10.1275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 3 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 85 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN C 445 GLN C 548 HIS D 141 ASN D 548 HIS D 563 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: 0.8305 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 26236 Z= 0.419 Angle : 1.762 16.309 36348 Z= 1.081 Chirality : 0.051 0.607 4071 Planarity : 0.017 0.136 4088 Dihedral : 21.092 98.680 4962 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 2.81 % 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: -1.36 (0.17), residues: 2664 helix: -2.23 (0.32), residues: 224 sheet: -2.13 (0.26), residues: 420 loop : -0.44 (0.14), residues: 2020 *********************** 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 222 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 152 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 30 residues processed: 203 average time/residue: 1.2185 time to fit residues: 296.7339 Evaluate side-chains 171 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 7 average time/residue: 0.4839 time to fit residues: 8.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 263 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 85 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 682 HIS C 257 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: 0.8248 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 26236 Z= 0.189 Angle : 1.702 15.517 36348 Z= 1.070 Chirality : 0.043 0.440 4071 Planarity : 0.016 0.123 4088 Dihedral : 21.064 100.029 4962 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 2.33 % 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: -1.16 (0.17), residues: 2664 helix: -1.82 (0.35), residues: 200 sheet: -2.00 (0.26), residues: 420 loop : -0.35 (0.14), residues: 2044 *********************** 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 203 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 145 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 30 residues processed: 188 average time/residue: 1.1466 time to fit residues: 260.5807 Evaluate side-chains 169 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 0.2917 time to fit residues: 5.4772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 149 optimal weight: 8.9990 chunk 192 optimal weight: 0.0970 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 85 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 26236 Z= 0.281 Angle : 1.703 15.506 36348 Z= 1.066 Chirality : 0.048 1.043 4071 Planarity : 0.017 0.130 4088 Dihedral : 21.194 101.587 4962 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 2.53 % 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: -1.24 (0.17), residues: 2664 helix: -2.08 (0.33), residues: 224 sheet: -2.06 (0.26), residues: 420 loop : -0.36 (0.15), residues: 2020 *********************** 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 207 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 144 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 33 residues processed: 192 average time/residue: 1.2222 time to fit residues: 280.0898 Evaluate side-chains 173 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 2.709 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 5 average time/residue: 0.5091 time to fit residues: 7.1743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 157 ASN A 287 ASN A 682 HIS B 169 GLN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 26236 Z= 0.413 Angle : 1.739 16.088 36348 Z= 1.074 Chirality : 0.052 0.724 4071 Planarity : 0.017 0.136 4088 Dihedral : 21.176 103.723 4962 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 2.73 % 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: -1.47 (0.17), residues: 2664 helix: -2.27 (0.31), residues: 224 sheet: -2.20 (0.26), residues: 420 loop : -0.53 (0.14), residues: 2020 *********************** 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 214 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 146 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 35 residues processed: 198 average time/residue: 1.2327 time to fit residues: 290.2541 Evaluate side-chains 177 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 2.714 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 0.2809 time to fit residues: 5.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 3.9990 chunk 251 optimal weight: 0.0770 chunk 229 optimal weight: 3.9990 chunk 244 optimal weight: 0.0070 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 26236 Z= 0.179 Angle : 1.678 15.323 36348 Z= 1.063 Chirality : 0.043 0.519 4071 Planarity : 0.016 0.123 4088 Dihedral : 21.207 104.552 4962 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 2.09 % 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: -1.22 (0.17), residues: 2664 helix: -1.89 (0.34), residues: 216 sheet: -2.02 (0.26), residues: 420 loop : -0.38 (0.15), residues: 2028 *********************** 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 199 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 30 residues processed: 190 average time/residue: 1.3080 time to fit residues: 297.2194 Evaluate side-chains 173 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 2.968 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.3267 time to fit residues: 4.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 0.7980 chunk 215 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 682 HIS B 599 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 26236 Z= 0.220 Angle : 1.670 15.158 36348 Z= 1.057 Chirality : 0.044 0.439 4071 Planarity : 0.016 0.126 4088 Dihedral : 21.342 105.624 4962 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 1.49 % 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: -1.20 (0.17), residues: 2664 helix: -1.84 (0.34), residues: 216 sheet: -2.00 (0.26), residues: 420 loop : -0.37 (0.15), residues: 2028 ********************** 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 180 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 32 residues processed: 174 average time/residue: 1.2668 time to fit residues: 262.1976 Evaluate side-chains 175 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.8267 time to fit residues: 5.6020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.0670 chunk 229 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.0670 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 287 ASN A 682 HIS C 257 ASN C 285 ASN C 457 ASN C 548 HIS C 678 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 = 0.4202 r_free = 0.4202 target = 0.170935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131340 restraints weight = 31206.773| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.80 r_work: 0.3578 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 26236 Z= 0.169 Angle : 1.641 15.214 36348 Z= 1.052 Chirality : 0.042 0.344 4071 Planarity : 0.016 0.122 4088 Dihedral : 21.430 105.987 4962 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.73 % 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: -1.09 (0.17), residues: 2664 helix: -1.75 (0.35), residues: 216 sheet: -1.90 (0.27), residues: 420 loop : -0.30 (0.15), residues: 2028 =============================================================================== Job complete usr+sys time: 7863.54 seconds wall clock time: 142 minutes 57.08 seconds (8577.08 seconds total)