Starting phenix.real_space_refine on Tue Mar 19 11:39:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuz_29482/03_2024/8fuz_29482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuz_29482/03_2024/8fuz_29482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuz_29482/03_2024/8fuz_29482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuz_29482/03_2024/8fuz_29482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuz_29482/03_2024/8fuz_29482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuz_29482/03_2024/8fuz_29482_updated.pdb" } resolution = 2.1 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= 0.237 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 15072 2.51 5 N 4096 2.21 5 O 4672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B ASP 315": "OD1" <-> "OD2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 315": "OD1" <-> "OD2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 418": "OD1" <-> "OD2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 418": "OD1" <-> "OD2" Residue "D ASP 449": "OD1" <-> "OD2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D GLU 500": "OE1" <-> "OE2" Residue "E ASP 3": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "E ASP 449": "OD1" <-> "OD2" Residue "E GLU 491": "OE1" <-> "OE2" Residue "E GLU 500": "OE1" <-> "OE2" Residue "F ASP 3": "OD1" <-> "OD2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ASP 315": "OD1" <-> "OD2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F GLU 487": "OE1" <-> "OE2" Residue "F GLU 510": "OE1" <-> "OE2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G ASP 315": "OD1" <-> "OD2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 418": "OD1" <-> "OD2" Residue "G ASP 449": "OD1" <-> "OD2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 261": "OD1" <-> "OD2" Residue "H ASP 315": "OD1" <-> "OD2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 418": "OD1" <-> "OD2" Residue "H ASP 449": "OD1" <-> "OD2" Residue "H GLU 487": "OE1" <-> "OE2" Residue "H GLU 491": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 24008 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "D" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "E" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "F" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "G" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "H" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} 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: 12.52, per 1000 atoms: 0.52 Number of scatterers: 24008 At special positions: 0 Unit cell: (134.88, 135.723, 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 4672 8.00 N 4096 7.00 C 15072 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: 9.87 Conformation dependent library (CDL) restraints added in 4.5 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 32 sheets defined 36.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 No H-bonds generated for 'chain 'A' and resid 2 through 5' Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.019A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'B' and resid 2 through 5 No H-bonds generated for 'chain 'B' and resid 2 through 5' Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.019A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid 2 through 5 No H-bonds generated for 'chain 'C' and resid 2 through 5' Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 254 through 266 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.020A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 2 through 5 No H-bonds generated for 'chain 'D' and resid 2 through 5' Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 254 through 266 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.023A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'E' and resid 2 through 5 No H-bonds generated for 'chain 'E' and resid 2 through 5' Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 254 through 266 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.022A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 421 Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 2 through 5 No H-bonds generated for 'chain 'F' and resid 2 through 5' Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 254 through 266 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.017A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'G' and resid 2 through 5 No H-bonds generated for 'chain 'G' and resid 2 through 5' Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 254 through 266 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.020A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 417 through 421 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid 2 through 5 No H-bonds generated for 'chain 'H' and resid 2 through 5' Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 254 through 266 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.020A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 421 Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.233A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.680A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 408 through 412 Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.231A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.678A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 408 through 412 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.228A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.682A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 408 through 412 Processing sheet with id= M, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.223A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.678A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 401 through 403 Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.231A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.679A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 401 through 403 Processing sheet with id= U, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.234A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.681A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 408 through 412 Processing sheet with id= Y, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.233A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.678A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 401 through 403 Processing sheet with id= AC, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.233A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.679A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 408 through 412 731 hydrogen bonds defined for protein. 1941 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: 7.55 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4009 1.30 - 1.43: 6117 1.43 - 1.56: 14025 1.56 - 1.69: 33 1.69 - 1.82: 240 Bond restraints: 24424 Sorted by residual: bond pdb=" C5 IMP B 601 " pdb=" C6 IMP B 601 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+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 4.78e+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 4.77e+01 bond pdb=" C5 IMP A 601 " pdb=" C6 IMP A 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 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 4.75e+01 ... (remaining 24419 not shown) Histogram of bond angle deviations from ideal: 94.27 - 102.72: 195 102.72 - 111.18: 9488 111.18 - 119.63: 11677 119.63 - 128.09: 11562 128.09 - 136.55: 118 Bond angle restraints: 33040 Sorted by residual: angle pdb=" N ASP A 274 " pdb=" CA ASP A 274 " pdb=" C ASP A 274 " ideal model delta sigma weight residual 108.23 116.70 -8.47 1.72e+00 3.38e-01 2.43e+01 angle pdb=" N ASP D 274 " pdb=" CA ASP D 274 " pdb=" C ASP D 274 " ideal model delta sigma weight residual 108.23 116.70 -8.47 1.72e+00 3.38e-01 2.43e+01 angle pdb=" N ASP F 274 " pdb=" CA ASP F 274 " pdb=" C ASP F 274 " ideal model delta sigma weight residual 107.99 116.65 -8.66 1.76e+00 3.23e-01 2.42e+01 angle pdb=" N ASP C 274 " pdb=" CA ASP C 274 " pdb=" C ASP C 274 " ideal model delta sigma weight residual 107.99 116.61 -8.62 1.76e+00 3.23e-01 2.40e+01 angle pdb=" N ASP E 274 " pdb=" CA ASP E 274 " pdb=" C ASP E 274 " ideal model delta sigma weight residual 107.99 116.59 -8.60 1.76e+00 3.23e-01 2.38e+01 ... (remaining 33035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.64: 13651 25.64 - 51.27: 985 51.27 - 76.91: 166 76.91 - 102.54: 46 102.54 - 128.18: 8 Dihedral angle restraints: 14856 sinusoidal: 6032 harmonic: 8824 Sorted by residual: dihedral pdb=" C5' IMP B 601 " pdb=" O5' IMP B 601 " pdb=" P IMP B 601 " pdb=" O2P IMP B 601 " ideal model delta sinusoidal sigma weight residual -168.07 -39.89 -128.18 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" C5' IMP E 601 " pdb=" O5' IMP E 601 " pdb=" P IMP E 601 " pdb=" O2P IMP E 601 " ideal model delta sinusoidal sigma weight residual 191.93 71.57 120.36 1 2.00e+01 2.50e-03 3.61e+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 73.06 118.87 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 14853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2801 0.057 - 0.114: 854 0.114 - 0.170: 93 0.170 - 0.227: 16 0.227 - 0.284: 4 Chirality restraints: 3768 Sorted by residual: chirality pdb=" C3D NAD B 602 " pdb=" C2D NAD B 602 " pdb=" C4D NAD B 602 " pdb=" O3D NAD B 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ASP G 28 " pdb=" N ASP G 28 " pdb=" C ASP G 28 " pdb=" CB ASP G 28 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASP D 28 " pdb=" N ASP D 28 " pdb=" C ASP D 28 " pdb=" CB ASP D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3765 not shown) Planarity restraints: 4176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 230 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASN A 230 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 230 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 231 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 26 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C CYS F 26 " -0.032 2.00e-02 2.50e+03 pdb=" O CYS F 26 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY F 27 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 26 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C CYS C 26 " 0.032 2.00e-02 2.50e+03 pdb=" O CYS C 26 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 27 " -0.011 2.00e-02 2.50e+03 ... (remaining 4173 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4150 2.77 - 3.30: 22961 3.30 - 3.83: 42495 3.83 - 4.37: 52540 4.37 - 4.90: 84534 Nonbonded interactions: 206680 Sorted by model distance: nonbonded pdb=" NH1 ARG B 512 " pdb=" OD1 ASP C 418 " model vdw 2.232 2.520 nonbonded pdb=" NH1 ARG F 512 " pdb=" OD1 ASP G 418 " model vdw 2.275 2.520 nonbonded pdb=" OD1 ASP E 418 " pdb=" NH1 ARG H 512 " model vdw 2.282 2.520 nonbonded pdb=" NH1 ARG E 512 " pdb=" OD1 ASP F 418 " model vdw 2.284 2.520 nonbonded pdb=" OG1 THR A 31 " pdb=" OE2 GLU D 500 " model vdw 2.319 2.440 ... (remaining 206675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 14.020 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 63.040 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 96.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 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 : 0.007 0.139 24424 Z= 0.489 Angle : 0.861 11.737 33040 Z= 0.425 Chirality : 0.053 0.284 3768 Planarity : 0.005 0.054 4176 Dihedral : 18.075 128.180 9256 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.17 % Allowed : 19.57 % Favored : 79.26 % 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: 0.92 (0.16), residues: 3072 helix: 1.72 (0.15), residues: 1200 sheet: 0.03 (0.23), residues: 432 loop : -0.08 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 454 PHE 0.018 0.003 PHE E 401 TYR 0.016 0.002 TYR A 353 ARG 0.007 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 445 time to evaluate : 2.665 Fit side-chains REVERT: A 1 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5982 (mpt) REVERT: C 78 MET cc_start: 0.9259 (tpp) cc_final: 0.8937 (tpp) REVERT: D 1 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6017 (mpt) REVERT: E 78 MET cc_start: 0.9266 (tpp) cc_final: 0.8962 (tpp) REVERT: E 230 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7371 (p0) REVERT: F 1 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6180 (mpt) REVERT: G 1 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6066 (mpt) REVERT: G 78 MET cc_start: 0.9265 (tpp) cc_final: 0.8974 (tpp) REVERT: H 1 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6089 (mpt) REVERT: H 78 MET cc_start: 0.9259 (tpp) cc_final: 0.8946 (tpp) outliers start: 29 outliers final: 16 residues processed: 463 average time/residue: 1.7397 time to fit residues: 896.3412 Evaluate side-chains 414 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 392 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 230 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 291 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.5980 chunk 236 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 33 ASN A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 33 ASN B 283 GLN B 368 GLN C 21 GLN C 33 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 21 GLN D 33 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 21 GLN E 33 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 33 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 21 GLN G 33 ASN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 21 GLN H 33 ASN H 94 ASN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 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 : 0.002 0.021 24424 Z= 0.146 Angle : 0.482 4.734 33040 Z= 0.260 Chirality : 0.042 0.146 3768 Planarity : 0.004 0.035 4176 Dihedral : 10.416 98.846 3888 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.65 % Allowed : 19.21 % Favored : 78.14 % 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: 0.92 (0.15), residues: 3072 helix: 1.68 (0.15), residues: 1224 sheet: 0.08 (0.23), residues: 432 loop : -0.09 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 454 PHE 0.010 0.001 PHE A 24 TYR 0.013 0.001 TYR G 353 ARG 0.003 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 408 time to evaluate : 2.829 Fit side-chains REVERT: A 1 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6533 (mmt) REVERT: C 78 MET cc_start: 0.9316 (tpp) cc_final: 0.9003 (tpp) REVERT: C 230 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7117 (p0) REVERT: E 78 MET cc_start: 0.9346 (tpp) cc_final: 0.9052 (tpp) REVERT: F 1 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6500 (mmt) REVERT: F 335 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: G 78 MET cc_start: 0.9344 (tpp) cc_final: 0.9056 (tpp) REVERT: H 78 MET cc_start: 0.9321 (tpp) cc_final: 0.9015 (tpp) outliers start: 66 outliers final: 20 residues processed: 447 average time/residue: 1.7443 time to fit residues: 877.5821 Evaluate side-chains 404 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 380 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 235 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 252 optimal weight: 0.8980 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 21 GLN B 48 GLN B 283 GLN B 368 GLN C 21 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 21 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24424 Z= 0.193 Angle : 0.523 5.008 33040 Z= 0.280 Chirality : 0.043 0.146 3768 Planarity : 0.004 0.038 4176 Dihedral : 10.139 101.847 3859 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.09 % Allowed : 18.45 % Favored : 78.46 % 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: 0.82 (0.15), residues: 3072 helix: 1.52 (0.15), residues: 1224 sheet: -0.00 (0.23), residues: 432 loop : -0.05 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 93 PHE 0.013 0.001 PHE E 24 TYR 0.014 0.002 TYR B 353 ARG 0.004 0.000 ARG E 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 391 time to evaluate : 2.471 Fit side-chains REVERT: A 1 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6486 (mmt) REVERT: A 335 GLU cc_start: 0.7720 (mp0) cc_final: 0.7500 (mp0) REVERT: C 291 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8413 (mptt) REVERT: D 112 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7295 (mm-40) REVERT: E 78 MET cc_start: 0.9376 (tpp) cc_final: 0.9092 (tpp) REVERT: F 335 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: G 78 MET cc_start: 0.9374 (tpp) cc_final: 0.9092 (tpp) REVERT: G 112 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7290 (mm-40) REVERT: H 335 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7504 (mp0) outliers start: 77 outliers final: 26 residues processed: 448 average time/residue: 1.6204 time to fit residues: 813.2009 Evaluate side-chains 402 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 370 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 284 optimal weight: 0.0070 chunk 301 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN B 243 GLN B 368 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 283 GLN E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 24424 Z= 0.150 Angle : 0.476 4.530 33040 Z= 0.256 Chirality : 0.042 0.142 3768 Planarity : 0.004 0.035 4176 Dihedral : 9.791 96.934 3852 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.89 % Allowed : 18.69 % Favored : 78.42 % 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: 0.83 (0.15), residues: 3072 helix: 1.54 (0.15), residues: 1224 sheet: -0.18 (0.23), residues: 424 loop : 0.02 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 93 PHE 0.010 0.001 PHE A 24 TYR 0.013 0.001 TYR A 353 ARG 0.003 0.000 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 397 time to evaluate : 2.679 Fit side-chains REVERT: A 1 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6462 (mmt) REVERT: B 241 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7824 (mtpt) REVERT: B 447 VAL cc_start: 0.8933 (m) cc_final: 0.8704 (t) REVERT: C 447 VAL cc_start: 0.8938 (m) cc_final: 0.8682 (t) REVERT: F 335 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: F 447 VAL cc_start: 0.8947 (m) cc_final: 0.8706 (t) REVERT: G 112 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7296 (mm-40) REVERT: H 335 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: H 447 VAL cc_start: 0.8929 (m) cc_final: 0.8698 (t) outliers start: 72 outliers final: 31 residues processed: 448 average time/residue: 1.6925 time to fit residues: 856.0761 Evaluate side-chains 399 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 364 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 224 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 153 optimal weight: 0.2980 chunk 270 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN B 243 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN E 283 GLN E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24424 Z= 0.171 Angle : 0.494 4.468 33040 Z= 0.265 Chirality : 0.042 0.143 3768 Planarity : 0.004 0.035 4176 Dihedral : 9.826 97.825 3852 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.65 % Allowed : 19.09 % Favored : 78.26 % 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: 0.81 (0.15), residues: 3072 helix: 1.52 (0.15), residues: 1224 sheet: -0.19 (0.23), residues: 424 loop : 0.01 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 93 PHE 0.018 0.001 PHE G 401 TYR 0.013 0.002 TYR H 353 ARG 0.004 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 376 time to evaluate : 2.659 Fit side-chains REVERT: A 1 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6512 (mmt) REVERT: A 447 VAL cc_start: 0.8945 (m) cc_final: 0.8730 (t) REVERT: B 241 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7834 (mtpt) REVERT: B 447 VAL cc_start: 0.8963 (m) cc_final: 0.8753 (t) REVERT: C 447 VAL cc_start: 0.8948 (m) cc_final: 0.8737 (t) REVERT: F 335 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: H 335 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7530 (mp0) outliers start: 66 outliers final: 35 residues processed: 427 average time/residue: 1.6537 time to fit residues: 790.6605 Evaluate side-chains 405 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 367 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.7980 chunk 271 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 0.0980 chunk 250 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 0.2980 chunk 158 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 243 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN E 283 GLN E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24424 Z= 0.123 Angle : 0.442 4.173 33040 Z= 0.237 Chirality : 0.041 0.139 3768 Planarity : 0.004 0.035 4176 Dihedral : 9.358 90.894 3850 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.53 % Allowed : 18.93 % Favored : 78.54 % 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: 0.89 (0.15), residues: 3072 helix: 1.62 (0.15), residues: 1224 sheet: -0.12 (0.23), residues: 424 loop : 0.00 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 92 PHE 0.016 0.001 PHE G 401 TYR 0.012 0.001 TYR G 353 ARG 0.003 0.000 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 402 time to evaluate : 2.306 Fit side-chains REVERT: B 241 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7824 (mtpt) REVERT: C 512 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6958 (mtm-85) REVERT: F 335 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7522 (mp0) outliers start: 63 outliers final: 26 residues processed: 449 average time/residue: 1.6002 time to fit residues: 810.2787 Evaluate side-chains 411 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 383 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24424 Z= 0.206 Angle : 0.529 4.907 33040 Z= 0.282 Chirality : 0.044 0.159 3768 Planarity : 0.004 0.037 4176 Dihedral : 9.870 102.419 3847 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.77 % Allowed : 18.69 % Favored : 78.54 % 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: 3072 helix: 1.49 (0.15), residues: 1224 sheet: -0.16 (0.23), residues: 424 loop : 0.01 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 93 PHE 0.018 0.002 PHE F 401 TYR 0.014 0.002 TYR F 353 ARG 0.004 0.000 ARG E 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 374 time to evaluate : 2.370 Fit side-chains REVERT: A 330 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9069 (pp) REVERT: A 335 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: B 241 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7831 (mtpt) REVERT: B 330 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9076 (pp) REVERT: C 330 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9062 (pp) REVERT: C 335 GLU cc_start: 0.7695 (mp0) cc_final: 0.7472 (mp0) REVERT: C 512 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7052 (mtm-85) REVERT: D 330 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9078 (pp) REVERT: E 330 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9064 (pp) REVERT: F 330 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9054 (pp) REVERT: F 335 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: G 330 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9064 (pp) REVERT: H 330 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.8923 (pp) REVERT: H 335 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7519 (mp0) outliers start: 69 outliers final: 34 residues processed: 427 average time/residue: 1.6476 time to fit residues: 785.3271 Evaluate side-chains 409 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 363 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 204 optimal weight: 0.1980 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 0.0010 chunk 236 optimal weight: 9.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24424 Z= 0.136 Angle : 0.462 4.393 33040 Z= 0.247 Chirality : 0.041 0.140 3768 Planarity : 0.004 0.035 4176 Dihedral : 9.428 94.208 3847 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.29 % Allowed : 19.37 % Favored : 78.34 % 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: 0.86 (0.15), residues: 3072 helix: 1.56 (0.15), residues: 1224 sheet: -0.11 (0.23), residues: 424 loop : 0.02 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 93 PHE 0.017 0.001 PHE A 401 TYR 0.012 0.001 TYR F 353 ARG 0.002 0.000 ARG G 407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 382 time to evaluate : 2.699 Fit side-chains REVERT: B 241 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7816 (mtpt) REVERT: C 335 GLU cc_start: 0.7661 (mp0) cc_final: 0.7437 (mp0) REVERT: C 512 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7014 (mtm-85) REVERT: F 335 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: H 335 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7510 (mp0) outliers start: 57 outliers final: 29 residues processed: 432 average time/residue: 1.6452 time to fit residues: 795.1573 Evaluate side-chains 393 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 361 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 0.0010 chunk 122 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 265 optimal weight: 0.0050 chunk 279 optimal weight: 0.9980 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24424 Z= 0.155 Angle : 0.484 4.544 33040 Z= 0.258 Chirality : 0.042 0.141 3768 Planarity : 0.004 0.035 4176 Dihedral : 9.480 94.753 3847 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.97 % Allowed : 19.77 % Favored : 78.26 % 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: 0.86 (0.15), residues: 3072 helix: 1.55 (0.15), residues: 1224 sheet: -0.12 (0.23), residues: 424 loop : 0.03 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 93 PHE 0.017 0.001 PHE F 401 TYR 0.013 0.001 TYR A 353 ARG 0.003 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 364 time to evaluate : 2.629 Fit side-chains REVERT: C 335 GLU cc_start: 0.7678 (mp0) cc_final: 0.7450 (mp0) REVERT: C 512 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7011 (mtm-85) REVERT: F 335 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: H 330 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.8981 (pp) REVERT: H 335 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7501 (mp0) outliers start: 49 outliers final: 31 residues processed: 404 average time/residue: 1.6112 time to fit residues: 729.9312 Evaluate side-chains 393 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 358 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24424 Z= 0.191 Angle : 0.527 5.404 33040 Z= 0.281 Chirality : 0.043 0.143 3768 Planarity : 0.004 0.037 4176 Dihedral : 9.768 101.414 3847 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.77 % Allowed : 19.94 % Favored : 78.30 % 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: 0.78 (0.15), residues: 3072 helix: 1.48 (0.15), residues: 1224 sheet: -0.17 (0.23), residues: 424 loop : 0.00 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 93 PHE 0.017 0.002 PHE C 401 TYR 0.014 0.002 TYR H 353 ARG 0.003 0.000 ARG G 407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 364 time to evaluate : 2.717 Fit side-chains REVERT: C 335 GLU cc_start: 0.7700 (mp0) cc_final: 0.7469 (mp0) REVERT: C 512 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7057 (mtm-85) REVERT: F 335 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: H 330 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.8991 (pp) REVERT: H 335 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7533 (mp0) outliers start: 44 outliers final: 35 residues processed: 402 average time/residue: 1.6742 time to fit residues: 753.6330 Evaluate side-chains 394 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 355 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.0070 chunk 263 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN F 283 GLN F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.098946 restraints weight = 22021.779| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.24 r_work: 0.2968 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24424 Z= 0.305 Angle : 0.623 5.339 33040 Z= 0.332 Chirality : 0.047 0.151 3768 Planarity : 0.005 0.050 4176 Dihedral : 10.272 109.900 3847 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.85 % Allowed : 20.06 % Favored : 78.09 % 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: 0.61 (0.15), residues: 3072 helix: 1.31 (0.15), residues: 1224 sheet: -0.26 (0.23), residues: 424 loop : -0.07 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 93 PHE 0.016 0.002 PHE F 401 TYR 0.016 0.002 TYR E 353 ARG 0.004 0.001 ARG G 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11854.36 seconds wall clock time: 209 minutes 55.49 seconds (12595.49 seconds total)