Starting phenix.real_space_refine on Thu Aug 8 18:43:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/08_2024/8foz_29357.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/08_2024/8foz_29357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/08_2024/8foz_29357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/08_2024/8foz_29357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/08_2024/8foz_29357.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/08_2024/8foz_29357.cif" } resolution = 2.0 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= 0.000 sd= 0.227 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 24 5.49 5 S 144 5.16 5 C 14832 2.51 5 N 4040 2.21 5 O 4608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 16": "OD1" <-> "OD2" Residue "A ASP 28": "OD1" <-> "OD2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 435": "OD1" <-> "OD2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ASP 315": "OD1" <-> "OD2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B ASP 435": "OD1" <-> "OD2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C ASP 315": "OD1" <-> "OD2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ASP 418": "OD1" <-> "OD2" Residue "C ASP 421": "OD1" <-> "OD2" Residue "C ASP 435": "OD1" <-> "OD2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ASP 418": "OD1" <-> "OD2" Residue "D ASP 421": "OD1" <-> "OD2" Residue "D ASP 435": "OD1" <-> "OD2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E ASP 255": "OD1" <-> "OD2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "E ASP 421": "OD1" <-> "OD2" Residue "E ASP 435": "OD1" <-> "OD2" Residue "E GLU 487": "OE1" <-> "OE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F ASP 28": "OD1" <-> "OD2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F ASP 315": "OD1" <-> "OD2" Residue "F ASP 319": "OD1" <-> "OD2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ASP 364": "OD1" <-> "OD2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F ASP 421": "OD1" <-> "OD2" Residue "F ASP 435": "OD1" <-> "OD2" Residue "F GLU 487": "OE1" <-> "OE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G GLU 254": "OE1" <-> "OE2" Residue "G ASP 255": "OD1" <-> "OD2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G ASP 292": "OD1" <-> "OD2" Residue "G ASP 315": "OD1" <-> "OD2" Residue "G ASP 319": "OD1" <-> "OD2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ASP 364": "OD1" <-> "OD2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ASP 421": "OD1" <-> "OD2" Residue "G ASP 435": "OD1" <-> "OD2" Residue "G GLU 487": "OE1" <-> "OE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H ASP 28": "OD1" <-> "OD2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 239": "OD1" <-> "OD2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H ASP 269": "OD1" <-> "OD2" Residue "H ASP 315": "OD1" <-> "OD2" Residue "H ASP 319": "OD1" <-> "OD2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ASP 364": "OD1" <-> "OD2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H ASP 418": "OD1" <-> "OD2" Residue "H ASP 421": "OD1" <-> "OD2" Residue "H ASP 435": "OD1" <-> "OD2" Residue "H GLU 487": "OE1" <-> "OE2" Residue "H GLU 500": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23648 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "B" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "C" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "D" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "E" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "F" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "G" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "H" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 13.94, per 1000 atoms: 0.59 Number of scatterers: 23648 At special positions: 0 Unit cell: (122.235, 122.235, 120.549, 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 144 16.00 P 24 15.00 O 4608 8.00 N 4040 7.00 C 14832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.57 Conformation dependent library (CDL) restraints added in 4.1 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 32 sheets defined 43.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.270A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.534A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.266A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.542A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 110 Processing helix chain 'C' and resid 254 through 267 removed outlier: 4.268A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.538A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.269A pdb=" N TYR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.539A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 356 removed outlier: 4.025A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 110 Processing helix chain 'E' and resid 254 through 267 removed outlier: 4.268A pdb=" N TYR E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.535A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 254 through 267 removed outlier: 4.265A pdb=" N TYR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.537A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 254 through 267 removed outlier: 4.267A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.541A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 356 removed outlier: 4.025A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 110 Processing helix chain 'H' and resid 254 through 267 removed outlier: 4.259A pdb=" N TYR H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.533A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 416 through 421 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.175A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.511A pdb=" N ILE A 406 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.659A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.168A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.661A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.177A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.646A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.181A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 4.173A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.658A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.661A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 4.168A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.645A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 4.174A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.654A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 4.165A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.85 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3952 1.30 - 1.43: 5962 1.43 - 1.56: 13870 1.56 - 1.69: 40 1.69 - 1.82: 240 Bond restraints: 24064 Sorted by residual: bond pdb=" C5 IMP A 601 " pdb=" C6 IMP A 601 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C5 IMP E 601 " pdb=" C6 IMP E 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP H 601 " pdb=" C6 IMP H 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP G 601 " pdb=" C6 IMP G 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP D 601 " pdb=" C6 IMP D 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 24059 not shown) Histogram of bond angle deviations from ideal: 97.12 - 104.89: 475 104.89 - 112.65: 12504 112.65 - 120.42: 10300 120.42 - 128.19: 9155 128.19 - 135.95: 134 Bond angle restraints: 32568 Sorted by residual: angle pdb=" N GLY G 9 " pdb=" CA GLY G 9 " pdb=" C GLY G 9 " ideal model delta sigma weight residual 110.77 104.64 6.13 1.93e+00 2.68e-01 1.01e+01 angle pdb=" N GLY D 9 " pdb=" CA GLY D 9 " pdb=" C GLY D 9 " ideal model delta sigma weight residual 110.77 104.68 6.09 1.93e+00 2.68e-01 9.97e+00 angle pdb=" N GLY H 9 " pdb=" CA GLY H 9 " pdb=" C GLY H 9 " ideal model delta sigma weight residual 110.77 104.70 6.07 1.93e+00 2.68e-01 9.90e+00 angle pdb=" N GLY A 9 " pdb=" CA GLY A 9 " pdb=" C GLY A 9 " ideal model delta sigma weight residual 110.77 104.76 6.01 1.93e+00 2.68e-01 9.69e+00 angle pdb=" N GLY C 9 " pdb=" CA GLY C 9 " pdb=" C GLY C 9 " ideal model delta sigma weight residual 110.77 104.78 5.99 1.93e+00 2.68e-01 9.64e+00 ... (remaining 32563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 13768 26.09 - 52.18: 757 52.18 - 78.27: 80 78.27 - 104.36: 31 104.36 - 130.45: 4 Dihedral angle restraints: 14640 sinusoidal: 5944 harmonic: 8696 Sorted by residual: dihedral pdb=" C5' IMP H 601 " pdb=" O5' IMP H 601 " pdb=" P IMP H 601 " pdb=" O2P IMP H 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.48 130.45 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" C5' IMP F 601 " pdb=" O5' IMP F 601 " pdb=" P IMP F 601 " pdb=" O2P IMP F 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.65 130.28 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.69 130.24 1 2.00e+01 2.50e-03 3.95e+01 ... (remaining 14637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2735 0.064 - 0.127: 884 0.127 - 0.191: 70 0.191 - 0.254: 15 0.254 - 0.318: 8 Chirality restraints: 3712 Sorted by residual: chirality pdb=" CB VAL E 361 " pdb=" CA VAL E 361 " pdb=" CG1 VAL E 361 " pdb=" CG2 VAL E 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL H 361 " pdb=" CA VAL H 361 " pdb=" CG1 VAL H 361 " pdb=" CG2 VAL H 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB VAL A 361 " pdb=" CA VAL A 361 " pdb=" CG1 VAL A 361 " pdb=" CG2 VAL A 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3709 not shown) Planarity restraints: 4120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 4 " 0.021 2.00e-02 2.50e+03 1.61e-02 5.19e+00 pdb=" CG TYR E 4 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 4 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR E 4 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 4 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 4 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 4 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 4 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 4 " -0.021 2.00e-02 2.50e+03 1.60e-02 5.14e+00 pdb=" CG TYR D 4 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 4 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 4 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 4 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 4 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 4 " -0.021 2.00e-02 2.50e+03 1.60e-02 5.11e+00 pdb=" CG TYR A 4 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 4 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 4 " -0.000 2.00e-02 2.50e+03 ... (remaining 4117 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4508 2.77 - 3.30: 22596 3.30 - 3.84: 41452 3.84 - 4.37: 50664 4.37 - 4.90: 83912 Nonbonded interactions: 203132 Sorted by model distance: nonbonded pdb=" OD1 ASP A 418 " pdb=" NH1 ARG D 512 " model vdw 2.238 3.120 nonbonded pdb=" NH1 ARG G 512 " pdb=" OD1 ASP H 418 " model vdw 2.240 3.120 nonbonded pdb=" NH1 ARG A 512 " pdb=" OD1 ASP B 418 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASP E 418 " pdb=" NH1 ARG H 512 " model vdw 2.260 3.120 nonbonded pdb=" NH1 ARG E 512 " pdb=" OD1 ASP F 418 " model vdw 2.268 3.120 ... (remaining 203127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 7.270 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: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 64.400 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 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:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.139 24064 Z= 0.595 Angle : 0.919 9.180 32568 Z= 0.483 Chirality : 0.059 0.318 3712 Planarity : 0.005 0.040 4120 Dihedral : 15.789 130.450 9120 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.31 % Allowed : 8.91 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.22 (0.15), residues: 3024 helix: 0.71 (0.14), residues: 1232 sheet: -0.42 (0.24), residues: 384 loop : -0.05 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 466 PHE 0.019 0.004 PHE G 24 TYR 0.039 0.004 TYR E 4 ARG 0.005 0.001 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 369 time to evaluate : 2.571 Fit side-chains REVERT: D 98 GLU cc_start: 0.8112 (mp0) cc_final: 0.7893 (mp0) REVERT: G 62 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8239 (mttt) REVERT: G 98 GLU cc_start: 0.8114 (mp0) cc_final: 0.7900 (mp0) REVERT: G 437 ILE cc_start: 0.8384 (mm) cc_final: 0.8176 (mp) outliers start: 32 outliers final: 24 residues processed: 397 average time/residue: 1.6124 time to fit residues: 715.8804 Evaluate side-chains 389 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 364 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24064 Z= 0.263 Angle : 0.611 4.880 32568 Z= 0.343 Chirality : 0.047 0.215 3712 Planarity : 0.004 0.030 4120 Dihedral : 10.692 115.088 3844 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.47 % Allowed : 7.92 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.60 (0.15), residues: 3024 helix: 1.18 (0.14), residues: 1240 sheet: -0.46 (0.23), residues: 384 loop : 0.08 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 466 PHE 0.014 0.003 PHE D 24 TYR 0.018 0.002 TYR G 4 ARG 0.003 0.001 ARG E 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 375 time to evaluate : 2.946 Fit side-chains REVERT: D 399 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7240 (tp30) outliers start: 36 outliers final: 31 residues processed: 405 average time/residue: 1.6871 time to fit residues: 762.4456 Evaluate side-chains 391 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 360 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 0.0570 chunk 187 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 276 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 246 optimal weight: 0.4980 chunk 274 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN E 265 GLN G 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 24064 Z= 0.143 Angle : 0.482 4.386 32568 Z= 0.271 Chirality : 0.041 0.145 3712 Planarity : 0.004 0.030 4120 Dihedral : 9.942 98.946 3840 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.04 % Allowed : 8.09 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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 (0.16), residues: 3024 helix: 1.77 (0.15), residues: 1240 sheet: -0.27 (0.24), residues: 384 loop : 0.29 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 466 PHE 0.010 0.002 PHE D 401 TYR 0.009 0.001 TYR A 353 ARG 0.002 0.000 ARG D 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 372 time to evaluate : 2.572 Fit side-chains REVERT: A 98 GLU cc_start: 0.8051 (mp0) cc_final: 0.7823 (mp0) REVERT: A 105 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7933 (ttp-170) REVERT: A 283 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.9102 (tt0) REVERT: B 283 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.9108 (tt0) REVERT: C 105 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7769 (ttm-80) REVERT: C 283 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.9107 (tt0) REVERT: C 450 LYS cc_start: 0.8395 (mttp) cc_final: 0.8185 (mttp) REVERT: D 283 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.9113 (tt0) REVERT: D 399 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7221 (tp30) REVERT: D 450 LYS cc_start: 0.8412 (mttp) cc_final: 0.8201 (mttp) REVERT: E 283 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9116 (tt0) REVERT: F 283 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9118 (tt0) REVERT: G 283 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.9118 (tt0) REVERT: H 283 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9115 (tt0) outliers start: 50 outliers final: 32 residues processed: 418 average time/residue: 1.6984 time to fit residues: 790.4806 Evaluate side-chains 408 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 368 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 293 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 21 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24064 Z= 0.224 Angle : 0.565 4.489 32568 Z= 0.316 Chirality : 0.044 0.161 3712 Planarity : 0.004 0.030 4120 Dihedral : 10.259 111.860 3840 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.80 % Allowed : 9.19 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.93 (0.15), residues: 3024 helix: 1.54 (0.15), residues: 1240 sheet: -0.28 (0.24), residues: 384 loop : 0.15 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 466 PHE 0.013 0.002 PHE F 24 TYR 0.013 0.002 TYR E 348 ARG 0.002 0.000 ARG F 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 365 time to evaluate : 2.577 Fit side-chains REVERT: C 450 LYS cc_start: 0.8375 (mttp) cc_final: 0.8171 (mttp) REVERT: D 399 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7264 (tp30) REVERT: F 450 LYS cc_start: 0.8346 (mttp) cc_final: 0.8078 (mttp) outliers start: 44 outliers final: 33 residues processed: 406 average time/residue: 1.7541 time to fit residues: 793.0164 Evaluate side-chains 416 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 383 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 250 optimal weight: 0.0670 chunk 203 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 263 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 overall best weight: 2.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24064 Z= 0.296 Angle : 0.628 5.136 32568 Z= 0.352 Chirality : 0.048 0.236 3712 Planarity : 0.004 0.029 4120 Dihedral : 10.441 116.194 3840 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.84 % Allowed : 9.56 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.66 (0.15), residues: 3024 helix: 1.26 (0.14), residues: 1240 sheet: -0.39 (0.24), residues: 384 loop : 0.07 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 466 PHE 0.016 0.003 PHE G 401 TYR 0.016 0.002 TYR C 4 ARG 0.004 0.001 ARG G 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 378 time to evaluate : 2.655 Fit side-chains REVERT: C 105 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7825 (ttm-80) REVERT: D 399 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7249 (tp30) REVERT: F 450 LYS cc_start: 0.8415 (mttp) cc_final: 0.8146 (mttp) outliers start: 45 outliers final: 32 residues processed: 419 average time/residue: 1.7216 time to fit residues: 802.4955 Evaluate side-chains 411 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 379 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 294 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24064 Z= 0.191 Angle : 0.529 4.388 32568 Z= 0.297 Chirality : 0.043 0.151 3712 Planarity : 0.004 0.030 4120 Dihedral : 10.120 106.321 3840 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.51 % Allowed : 9.52 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.97 (0.15), residues: 3024 helix: 1.58 (0.15), residues: 1240 sheet: -0.24 (0.24), residues: 384 loop : 0.17 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 466 PHE 0.011 0.002 PHE H 401 TYR 0.011 0.002 TYR A 348 ARG 0.002 0.000 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 365 time to evaluate : 2.921 Fit side-chains REVERT: C 450 LYS cc_start: 0.8378 (mttp) cc_final: 0.8160 (mttp) REVERT: D 399 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7232 (tp30) REVERT: D 450 LYS cc_start: 0.8411 (mttp) cc_final: 0.8179 (mttp) REVERT: F 450 LYS cc_start: 0.8372 (mttp) cc_final: 0.8130 (mttp) REVERT: G 491 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7917 (tt0) outliers start: 37 outliers final: 31 residues processed: 400 average time/residue: 1.7944 time to fit residues: 802.5461 Evaluate side-chains 409 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 377 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 247 optimal weight: 0.0050 chunk 164 optimal weight: 0.7980 chunk 293 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 135 optimal weight: 0.0870 overall best weight: 0.7374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 24064 Z= 0.150 Angle : 0.489 4.348 32568 Z= 0.274 Chirality : 0.041 0.144 3712 Planarity : 0.004 0.030 4120 Dihedral : 9.825 97.364 3840 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.80 % Allowed : 9.72 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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 (0.15), residues: 3024 helix: 1.76 (0.15), residues: 1240 sheet: -0.13 (0.24), residues: 384 loop : 0.24 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 466 PHE 0.010 0.002 PHE D 401 TYR 0.010 0.001 TYR F 353 ARG 0.002 0.000 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 358 time to evaluate : 2.610 Fit side-chains REVERT: D 105 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7968 (ttp-170) REVERT: D 399 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7226 (tp30) REVERT: D 450 LYS cc_start: 0.8372 (mttp) cc_final: 0.8156 (mttp) REVERT: F 450 LYS cc_start: 0.8312 (mttp) cc_final: 0.8105 (mttp) REVERT: G 491 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7882 (tt0) outliers start: 44 outliers final: 31 residues processed: 399 average time/residue: 1.7257 time to fit residues: 766.2841 Evaluate side-chains 388 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 356 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 21 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24064 Z= 0.264 Angle : 0.601 4.839 32568 Z= 0.336 Chirality : 0.046 0.198 3712 Planarity : 0.004 0.029 4120 Dihedral : 10.300 114.709 3840 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.35 % Allowed : 10.05 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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 (0.15), residues: 3024 helix: 1.40 (0.15), residues: 1240 sheet: -0.25 (0.24), residues: 384 loop : 0.09 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 466 PHE 0.014 0.002 PHE D 401 TYR 0.014 0.002 TYR A 348 ARG 0.003 0.001 ARG H 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 366 time to evaluate : 2.658 Fit side-chains REVERT: C 450 LYS cc_start: 0.8293 (mttp) cc_final: 0.8060 (mttp) REVERT: D 399 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7229 (tp30) REVERT: F 450 LYS cc_start: 0.8393 (mttp) cc_final: 0.8137 (mttp) REVERT: G 450 LYS cc_start: 0.8292 (mttp) cc_final: 0.8051 (mttp) outliers start: 33 outliers final: 32 residues processed: 397 average time/residue: 1.7304 time to fit residues: 765.4810 Evaluate side-chains 403 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 371 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 chunk 273 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 214 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 258 optimal weight: 0.0670 chunk 272 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24064 Z= 0.139 Angle : 0.485 4.315 32568 Z= 0.272 Chirality : 0.041 0.141 3712 Planarity : 0.003 0.031 4120 Dihedral : 9.774 97.488 3840 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 9.84 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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 (0.15), residues: 3024 helix: 1.76 (0.15), residues: 1240 sheet: -0.06 (0.24), residues: 384 loop : 0.22 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 466 PHE 0.010 0.002 PHE A 514 TYR 0.010 0.001 TYR B 353 ARG 0.003 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 362 time to evaluate : 2.572 Fit side-chains REVERT: C 450 LYS cc_start: 0.8158 (mttp) cc_final: 0.7956 (mttp) REVERT: D 105 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7949 (ttp-170) REVERT: D 399 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7218 (tp30) REVERT: D 450 LYS cc_start: 0.8363 (mttp) cc_final: 0.8131 (mttp) REVERT: G 491 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7873 (tt0) outliers start: 37 outliers final: 31 residues processed: 394 average time/residue: 1.7322 time to fit residues: 759.6690 Evaluate side-chains 381 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 349 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 7.9990 chunk 288 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 302 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 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 265 GLN A 441 GLN A 498 GLN B 265 GLN B 498 GLN C 265 GLN C 498 GLN D 21 GLN D 265 GLN D 498 GLN E 265 GLN E 441 GLN E 498 GLN F 265 GLN F 498 GLN G 21 GLN G 265 GLN H 265 GLN H 441 GLN H 498 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24064 Z= 0.365 Angle : 0.686 5.674 32568 Z= 0.383 Chirality : 0.051 0.279 3712 Planarity : 0.005 0.029 4120 Dihedral : 10.493 117.831 3840 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.63 % Allowed : 9.76 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.59 (0.15), residues: 3024 helix: 1.17 (0.14), residues: 1240 sheet: -0.33 (0.24), residues: 384 loop : 0.03 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 466 PHE 0.016 0.003 PHE E 401 TYR 0.019 0.003 TYR C 4 ARG 0.005 0.001 ARG H 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 358 time to evaluate : 2.910 Fit side-chains REVERT: D 105 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7950 (ttp-110) REVERT: D 399 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7249 (tp30) outliers start: 40 outliers final: 32 residues processed: 397 average time/residue: 1.4318 time to fit residues: 632.5862 Evaluate side-chains 389 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 357 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1339 > 50: distance: 47 - 54: 13.180 distance: 54 - 55: 20.435 distance: 55 - 56: 21.718 distance: 55 - 58: 36.123 distance: 56 - 57: 20.030 distance: 56 - 62: 13.624 distance: 57 - 83: 45.766 distance: 58 - 59: 8.345 distance: 59 - 60: 14.434 distance: 59 - 61: 17.786 distance: 62 - 63: 19.173 distance: 63 - 64: 18.301 distance: 63 - 66: 22.737 distance: 64 - 65: 4.366 distance: 64 - 69: 15.439 distance: 65 - 91: 26.343 distance: 66 - 67: 12.577 distance: 66 - 68: 12.920 distance: 69 - 70: 6.739 distance: 70 - 71: 10.912 distance: 71 - 72: 8.899 distance: 71 - 73: 6.324 distance: 72 - 96: 16.618 distance: 73 - 74: 17.510 distance: 74 - 75: 8.796 distance: 74 - 77: 8.493 distance: 75 - 83: 6.395 distance: 76 - 105: 17.577 distance: 77 - 78: 8.214 distance: 78 - 79: 6.057 distance: 78 - 80: 15.272 distance: 79 - 81: 29.179 distance: 80 - 82: 15.994 distance: 81 - 82: 6.889 distance: 83 - 84: 7.130 distance: 84 - 85: 6.923 distance: 84 - 87: 5.202 distance: 85 - 86: 9.797 distance: 85 - 91: 5.795 distance: 86 - 110: 14.496 distance: 87 - 88: 5.924 distance: 87 - 89: 26.187 distance: 88 - 90: 5.483 distance: 91 - 92: 24.184 distance: 92 - 93: 12.724 distance: 92 - 95: 6.748 distance: 93 - 94: 5.734 distance: 93 - 96: 24.725 distance: 94 - 118: 32.122 distance: 96 - 97: 6.330 distance: 97 - 98: 5.007 distance: 97 - 100: 15.177 distance: 98 - 99: 16.826 distance: 98 - 105: 11.954 distance: 99 - 123: 16.227 distance: 100 - 101: 15.965 distance: 101 - 102: 7.953 distance: 102 - 103: 15.711 distance: 103 - 104: 6.719 distance: 105 - 106: 12.447 distance: 106 - 107: 14.101 distance: 106 - 109: 16.797 distance: 107 - 108: 7.109 distance: 107 - 110: 18.222 distance: 110 - 111: 4.109 distance: 111 - 112: 18.677 distance: 111 - 114: 5.679 distance: 112 - 113: 14.458 distance: 112 - 118: 10.077 distance: 114 - 115: 15.440 distance: 115 - 116: 9.992 distance: 115 - 117: 26.067 distance: 118 - 119: 4.728 distance: 119 - 120: 10.336 distance: 119 - 122: 4.283 distance: 120 - 121: 6.514 distance: 120 - 123: 12.187