Starting phenix.real_space_refine on Mon Mar 18 14:40:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/03_2024/8p3p_17389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/03_2024/8p3p_17389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/03_2024/8p3p_17389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/03_2024/8p3p_17389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/03_2024/8p3p_17389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/03_2024/8p3p_17389.pdb" } resolution = 2.5 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= 0.011 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13408 2.51 5 N 3776 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 249": "OE1" <-> "OE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "F PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 249": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21224 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "H" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "A" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "B" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "F" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "G" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Time building chain proxies: 11.53, per 1000 atoms: 0.54 Number of scatterers: 21224 At special positions: 0 Unit cell: (123.372, 123.372, 169.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3920 8.00 N 3776 7.00 C 13408 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=0, symmetry=0 Time building additional restraints: 8.33 Conformation dependent library (CDL) restraints added in 3.9 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 70.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.704A pdb=" N ARG C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 50 removed outlier: 3.502A pdb=" N ILE C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.673A pdb=" N GLY C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 110 through 120 removed outlier: 3.685A pdb=" N GLN C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.679A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.687A pdb=" N ARG C 155 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 238 Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.737A pdb=" N VAL C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 removed outlier: 4.388A pdb=" N CYS C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 removed outlier: 3.628A pdb=" N ARG H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 50 removed outlier: 3.510A pdb=" N ILE H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 70 removed outlier: 3.801A pdb=" N GLY H 70 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 86 removed outlier: 3.745A pdb=" N SER H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 121 through 127 removed outlier: 3.699A pdb=" N ARG H 127 " --> pdb=" O TYR H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 167 through 237 removed outlier: 3.562A pdb=" N LEU H 175 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.673A pdb=" N MET H 256 " --> pdb=" O ASP H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 Processing helix chain 'H' and resid 279 through 295 removed outlier: 3.613A pdb=" N ASP H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY H 295 " --> pdb=" O THR H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 348 Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.704A pdb=" N ARG A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 50 removed outlier: 3.501A pdb=" N ILE A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.675A pdb=" N GLY A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.685A pdb=" N GLN A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.678A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.687A pdb=" N ARG A 155 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 238 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.737A pdb=" N VAL A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 346 removed outlier: 4.388A pdb=" N CYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.627A pdb=" N ARG B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 50 removed outlier: 3.511A pdb=" N ILE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.812A pdb=" N GLY B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 removed outlier: 3.745A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 121 through 127 removed outlier: 3.700A pdb=" N ARG B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 167 through 237 removed outlier: 3.562A pdb=" N LEU B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.677A pdb=" N MET B 256 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.613A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 348 Processing helix chain 'D' and resid 18 through 24 removed outlier: 3.704A pdb=" N ARG D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 50 removed outlier: 3.502A pdb=" N ILE D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.674A pdb=" N GLY D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 95 through 109 Processing helix chain 'D' and resid 110 through 120 removed outlier: 3.685A pdb=" N GLN D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 removed outlier: 3.677A pdb=" N ILE D 146 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.702A pdb=" N ARG D 155 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 238 Processing helix chain 'D' and resid 245 through 249 Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 279 through 294 removed outlier: 3.737A pdb=" N VAL D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 346 removed outlier: 4.388A pdb=" N CYS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 removed outlier: 3.628A pdb=" N ARG E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 50 removed outlier: 3.510A pdb=" N ILE E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.810A pdb=" N GLY E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.745A pdb=" N SER E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 110 Processing helix chain 'E' and resid 110 through 121 Processing helix chain 'E' and resid 121 through 127 removed outlier: 3.699A pdb=" N ARG E 127 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 167 through 237 removed outlier: 3.563A pdb=" N LEU E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.675A pdb=" N MET E 256 " --> pdb=" O ASP E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.612A pdb=" N ASP E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY E 295 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 348 Processing helix chain 'F' and resid 18 through 24 removed outlier: 3.703A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 50 removed outlier: 3.502A pdb=" N ILE F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 70 removed outlier: 3.673A pdb=" N GLY F 70 " --> pdb=" O ASN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 86 Processing helix chain 'F' and resid 95 through 109 Processing helix chain 'F' and resid 110 through 120 removed outlier: 3.685A pdb=" N GLN F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 146 removed outlier: 3.679A pdb=" N ILE F 146 " --> pdb=" O MET F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.688A pdb=" N ARG F 155 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 238 Processing helix chain 'F' and resid 245 through 249 Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 279 through 294 removed outlier: 3.737A pdb=" N VAL F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 346 removed outlier: 4.388A pdb=" N CYS F 346 " --> pdb=" O LEU F 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 removed outlier: 3.634A pdb=" N ARG G 24 " --> pdb=" O ARG G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 50 removed outlier: 3.509A pdb=" N ILE G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.812A pdb=" N GLY G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.734A pdb=" N SER G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'G' and resid 110 through 121 Processing helix chain 'G' and resid 121 through 127 removed outlier: 3.700A pdb=" N ARG G 127 " --> pdb=" O TYR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 167 through 237 removed outlier: 3.562A pdb=" N LEU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 removed outlier: 3.675A pdb=" N MET G 256 " --> pdb=" O ASP G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 275 Processing helix chain 'G' and resid 279 through 295 removed outlier: 3.612A pdb=" N ASP G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY G 295 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 348 Processing sheet with id=AA1, first strand: chain 'C' and resid 147 through 149 removed outlier: 6.127A pdb=" N ILE C 60 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.583A pdb=" N ASP H 62 " --> pdb=" O TYR H 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR H 307 " --> pdb=" O ASP H 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.128A pdb=" N ILE A 60 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 149 removed outlier: 6.585A pdb=" N ASP B 62 " --> pdb=" O TYR B 307 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR B 307 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 147 through 149 removed outlier: 6.128A pdb=" N ILE D 60 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.584A pdb=" N ASP E 62 " --> pdb=" O TYR E 307 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR E 307 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 147 through 149 removed outlier: 6.128A pdb=" N ILE F 60 " --> pdb=" O LEU F 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 146 through 149 removed outlier: 6.584A pdb=" N ASP G 62 " --> pdb=" O TYR G 307 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR G 307 " --> pdb=" O ASP G 62 " (cutoff:3.500A) 1520 hydrogen bonds defined for protein. 4416 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: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7180 1.35 - 1.46: 4896 1.46 - 1.58: 9340 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 21648 Sorted by residual: bond pdb=" N MET G 328 " pdb=" CA MET G 328 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.92e+00 bond pdb=" N MET E 328 " pdb=" CA MET E 328 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.92e+00 bond pdb=" N MET H 328 " pdb=" CA MET H 328 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.84e+00 bond pdb=" N MET B 328 " pdb=" CA MET B 328 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.84e+00 bond pdb=" CB GLU E 249 " pdb=" CG GLU E 249 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 ... (remaining 21643 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.56: 575 106.56 - 113.43: 11481 113.43 - 120.29: 7883 120.29 - 127.16: 9123 127.16 - 134.02: 234 Bond angle restraints: 29296 Sorted by residual: angle pdb=" CB MET G 224 " pdb=" CG MET G 224 " pdb=" SD MET G 224 " ideal model delta sigma weight residual 112.70 124.07 -11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CB MET H 224 " pdb=" CG MET H 224 " pdb=" SD MET H 224 " ideal model delta sigma weight residual 112.70 124.07 -11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CB MET B 224 " pdb=" CG MET B 224 " pdb=" SD MET B 224 " ideal model delta sigma weight residual 112.70 124.06 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET E 224 " pdb=" CG MET E 224 " pdb=" SD MET E 224 " ideal model delta sigma weight residual 112.70 124.03 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET D 256 " pdb=" CG MET D 256 " pdb=" SD MET D 256 " ideal model delta sigma weight residual 112.70 123.01 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 29291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 11331 17.83 - 35.67: 1398 35.67 - 53.50: 358 53.50 - 71.34: 53 71.34 - 89.17: 12 Dihedral angle restraints: 13152 sinusoidal: 5376 harmonic: 7776 Sorted by residual: dihedral pdb=" CA ASP C 92 " pdb=" CB ASP C 92 " pdb=" CG ASP C 92 " pdb=" OD1 ASP C 92 " ideal model delta sinusoidal sigma weight residual -30.00 -87.69 57.69 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP D 92 " pdb=" CB ASP D 92 " pdb=" CG ASP D 92 " pdb=" OD1 ASP D 92 " ideal model delta sinusoidal sigma weight residual -30.00 -87.66 57.66 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP F 92 " pdb=" CB ASP F 92 " pdb=" CG ASP F 92 " pdb=" OD1 ASP F 92 " ideal model delta sinusoidal sigma weight residual -30.00 -87.66 57.66 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 13149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1969 0.025 - 0.049: 740 0.049 - 0.074: 319 0.074 - 0.099: 110 0.099 - 0.124: 46 Chirality restraints: 3184 Sorted by residual: chirality pdb=" CA ILE H 149 " pdb=" N ILE H 149 " pdb=" C ILE H 149 " pdb=" CB ILE H 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE E 149 " pdb=" N ILE E 149 " pdb=" C ILE E 149 " pdb=" CB ILE E 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA MET H 68 " pdb=" N MET H 68 " pdb=" C MET H 68 " pdb=" CB MET H 68 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 3181 not shown) Planarity restraints: 3840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 249 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CD GLU B 249 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 249 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 249 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 249 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" CD GLU E 249 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU E 249 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU E 249 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 249 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" CD GLU H 249 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU H 249 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU H 249 " 0.012 2.00e-02 2.50e+03 ... (remaining 3837 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5045 2.79 - 3.32: 21116 3.32 - 3.85: 36383 3.85 - 4.37: 39611 4.37 - 4.90: 70005 Nonbonded interactions: 172160 Sorted by model distance: nonbonded pdb=" O LEU C 108 " pdb=" OH TYR C 178 " model vdw 2.267 2.440 nonbonded pdb=" O LEU D 108 " pdb=" OH TYR D 178 " model vdw 2.268 2.440 nonbonded pdb=" O LEU A 108 " pdb=" OH TYR A 178 " model vdw 2.269 2.440 nonbonded pdb=" O LEU F 108 " pdb=" OH TYR F 178 " model vdw 2.269 2.440 nonbonded pdb=" O GLY G 71 " pdb=" OG SER G 74 " model vdw 2.339 2.440 ... (remaining 172155 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 27.260 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 59.240 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.160 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.003 0.041 21648 Z= 0.190 Angle : 0.626 11.373 29296 Z= 0.300 Chirality : 0.035 0.124 3184 Planarity : 0.004 0.035 3840 Dihedral : 16.190 89.170 8112 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.86 % Allowed : 23.41 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.17), residues: 2640 helix: 3.22 (0.12), residues: 1760 sheet: 2.41 (0.50), residues: 156 loop : -0.77 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS F 237 PHE 0.027 0.001 PHE A 324 TYR 0.014 0.001 TYR C 123 ARG 0.009 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 ASP cc_start: 0.7350 (t0) cc_final: 0.7000 (t0) REVERT: A 152 ASP cc_start: 0.7346 (t0) cc_final: 0.6997 (t0) REVERT: D 155 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8529 (mpp80) REVERT: F 152 ASP cc_start: 0.7352 (t0) cc_final: 0.7003 (t0) outliers start: 19 outliers final: 12 residues processed: 204 average time/residue: 1.6266 time to fit residues: 369.5863 Evaluate side-chains 188 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 226 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.4980 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 239 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 ASN B 67 ASN E 67 ASN G 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21648 Z= 0.218 Angle : 0.539 7.112 29296 Z= 0.265 Chirality : 0.036 0.150 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.849 36.521 2968 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.72 % Allowed : 21.74 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.17), residues: 2640 helix: 3.52 (0.12), residues: 1776 sheet: 2.31 (0.59), residues: 112 loop : -0.68 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 111 HIS 0.003 0.001 HIS H 237 PHE 0.019 0.001 PHE D 324 TYR 0.017 0.001 TYR C 123 ARG 0.005 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 ASP cc_start: 0.7335 (t0) cc_final: 0.7115 (t0) REVERT: C 155 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8648 (mtm-85) REVERT: H 301 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7422 (mmp80) REVERT: A 152 ASP cc_start: 0.7318 (t0) cc_final: 0.7099 (t0) REVERT: A 155 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8650 (mtm-85) REVERT: B 301 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7423 (mmp80) REVERT: D 155 ARG cc_start: 0.8920 (mtm-85) cc_final: 0.8627 (mpp80) REVERT: E 301 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7425 (mmp80) REVERT: F 152 ASP cc_start: 0.7340 (t0) cc_final: 0.7121 (t0) REVERT: F 155 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8642 (mtm-85) REVERT: G 301 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7425 (mmp80) outliers start: 38 outliers final: 10 residues processed: 207 average time/residue: 1.5712 time to fit residues: 362.5881 Evaluate side-chains 199 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.0870 chunk 74 optimal weight: 0.6980 chunk 199 optimal weight: 0.0000 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 240 optimal weight: 0.5980 chunk 259 optimal weight: 0.0980 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21648 Z= 0.134 Angle : 0.504 7.402 29296 Z= 0.245 Chirality : 0.034 0.121 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.472 35.219 2958 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.95 % Allowed : 22.28 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.17), residues: 2640 helix: 3.63 (0.12), residues: 1776 sheet: 2.42 (0.49), residues: 156 loop : -0.69 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 111 HIS 0.000 0.000 HIS H 237 PHE 0.012 0.001 PHE C 181 TYR 0.013 0.001 TYR C 123 ARG 0.005 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 ASP cc_start: 0.7402 (t0) cc_final: 0.7151 (t0) REVERT: C 155 ARG cc_start: 0.8935 (mtm-85) cc_final: 0.8716 (mtm-85) REVERT: H 335 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6711 (mp) REVERT: A 152 ASP cc_start: 0.7410 (t0) cc_final: 0.7157 (t0) REVERT: A 155 ARG cc_start: 0.8937 (mtm-85) cc_final: 0.8717 (mtm-85) REVERT: B 335 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6712 (mp) REVERT: D 155 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8654 (mpp80) REVERT: E 335 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6711 (mp) REVERT: F 152 ASP cc_start: 0.7424 (t0) cc_final: 0.7169 (t0) REVERT: F 155 ARG cc_start: 0.8935 (mtm-85) cc_final: 0.8713 (mtm-85) REVERT: G 335 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6677 (mp) outliers start: 43 outliers final: 10 residues processed: 217 average time/residue: 1.3678 time to fit residues: 333.2491 Evaluate side-chains 197 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 307 TYR Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 307 TYR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 307 TYR Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 161 optimal weight: 0.0870 chunk 241 optimal weight: 0.5980 chunk 255 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 228 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21648 Z= 0.181 Angle : 0.528 7.856 29296 Z= 0.256 Chirality : 0.035 0.152 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.414 35.149 2956 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.81 % Allowed : 21.74 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.17), residues: 2640 helix: 3.66 (0.12), residues: 1776 sheet: 2.37 (0.49), residues: 156 loop : -0.65 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.001 0.000 HIS C 189 PHE 0.025 0.001 PHE C 324 TYR 0.015 0.001 TYR D 123 ARG 0.005 0.000 ARG H 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 190 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8935 (mtm-85) cc_final: 0.8579 (mpp80) REVERT: H 335 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6697 (mp) REVERT: A 155 ARG cc_start: 0.8935 (mtm-85) cc_final: 0.8576 (mpp80) REVERT: B 335 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6698 (mp) REVERT: E 335 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6697 (mp) REVERT: F 155 ARG cc_start: 0.8934 (mtm-85) cc_final: 0.8575 (mpp80) REVERT: G 335 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6695 (mp) outliers start: 62 outliers final: 12 residues processed: 225 average time/residue: 1.4483 time to fit residues: 365.2761 Evaluate side-chains 192 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 0.7980 chunk 229 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21648 Z= 0.214 Angle : 0.552 9.214 29296 Z= 0.263 Chirality : 0.035 0.121 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.502 36.293 2956 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.58 % Allowed : 22.42 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.17), residues: 2640 helix: 3.66 (0.12), residues: 1776 sheet: 2.35 (0.49), residues: 156 loop : -0.62 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.001 0.000 HIS D 189 PHE 0.013 0.001 PHE D 302 TYR 0.017 0.001 TYR D 123 ARG 0.009 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 191 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8470 (mpp80) REVERT: H 301 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7384 (mmp80) REVERT: H 335 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6697 (mp) REVERT: A 155 ARG cc_start: 0.8905 (mtm-85) cc_final: 0.8468 (mpp80) REVERT: B 63 ARG cc_start: 0.8400 (mtm110) cc_final: 0.8191 (mtp-110) REVERT: B 301 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7388 (mmp80) REVERT: B 335 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6699 (mp) REVERT: E 301 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7396 (mmp80) REVERT: E 335 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6699 (mp) REVERT: F 155 ARG cc_start: 0.8904 (mtm-85) cc_final: 0.8465 (mpp80) REVERT: G 301 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7392 (mmp80) REVERT: G 335 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6694 (mp) outliers start: 57 outliers final: 13 residues processed: 219 average time/residue: 1.5336 time to fit residues: 376.5705 Evaluate side-chains 198 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 1.9990 chunk 229 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21648 Z= 0.260 Angle : 0.573 8.621 29296 Z= 0.277 Chirality : 0.036 0.154 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.603 37.806 2956 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.22 % Favored : 96.63 % Rotamer: Outliers : 2.45 % Allowed : 23.10 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.17), residues: 2640 helix: 3.63 (0.12), residues: 1776 sheet: 2.29 (0.49), residues: 156 loop : -0.62 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.002 0.001 HIS H 237 PHE 0.027 0.002 PHE D 324 TYR 0.018 0.002 TYR C 123 ARG 0.010 0.000 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 185 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 301 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7348 (mmp80) REVERT: H 335 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6723 (mp) REVERT: B 301 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7353 (mmp80) REVERT: B 335 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6724 (mp) REVERT: E 301 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7358 (mmp80) REVERT: E 335 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6725 (mp) REVERT: G 301 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7357 (mmp80) REVERT: G 335 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6715 (mp) outliers start: 54 outliers final: 19 residues processed: 210 average time/residue: 1.5264 time to fit residues: 357.8259 Evaluate side-chains 201 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 159 optimal weight: 0.0770 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21648 Z= 0.169 Angle : 0.564 9.273 29296 Z= 0.267 Chirality : 0.034 0.121 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.501 37.451 2956 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 24.28 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.17), residues: 2640 helix: 3.68 (0.12), residues: 1776 sheet: 2.28 (0.50), residues: 156 loop : -0.66 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.003 0.000 HIS E 237 PHE 0.019 0.001 PHE A 153 TYR 0.014 0.001 TYR D 123 ARG 0.009 0.000 ARG E 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 ASP cc_start: 0.7547 (t0) cc_final: 0.7258 (t0) REVERT: C 155 ARG cc_start: 0.8966 (mpp80) cc_final: 0.8764 (mtm-85) REVERT: H 301 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7321 (mmp80) REVERT: B 301 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7332 (mmp80) REVERT: D 152 ASP cc_start: 0.7572 (t0) cc_final: 0.7346 (t0) REVERT: D 155 ARG cc_start: 0.8918 (mpp80) cc_final: 0.8516 (mpp80) REVERT: F 152 ASP cc_start: 0.7558 (t0) cc_final: 0.7269 (t0) REVERT: F 155 ARG cc_start: 0.8965 (mpp80) cc_final: 0.8762 (mtm-85) REVERT: G 301 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7336 (mmp80) outliers start: 37 outliers final: 15 residues processed: 207 average time/residue: 1.4858 time to fit residues: 344.3883 Evaluate side-chains 196 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 307 TYR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 307 TYR Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 307 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 200 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21648 Z= 0.235 Angle : 0.597 9.883 29296 Z= 0.284 Chirality : 0.036 0.148 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.566 38.032 2956 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.77 % Allowed : 24.55 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.17), residues: 2640 helix: 3.68 (0.12), residues: 1776 sheet: 2.26 (0.49), residues: 156 loop : -0.64 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.006 0.001 HIS E 237 PHE 0.028 0.002 PHE C 324 TYR 0.017 0.001 TYR D 123 ARG 0.007 0.000 ARG E 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 301 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7344 (mmp80) REVERT: H 335 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6697 (mp) REVERT: A 155 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8526 (mpp80) REVERT: B 301 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7349 (mmp80) REVERT: B 335 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6697 (mp) REVERT: D 81 ASN cc_start: 0.8514 (m110) cc_final: 0.8110 (m-40) REVERT: D 155 ARG cc_start: 0.8939 (mpp80) cc_final: 0.8690 (mpp80) REVERT: E 301 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7345 (mmp80) REVERT: E 335 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6698 (mp) REVERT: G 301 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7352 (mmp80) REVERT: G 335 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6694 (mp) outliers start: 39 outliers final: 16 residues processed: 204 average time/residue: 1.4966 time to fit residues: 342.1119 Evaluate side-chains 201 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 214 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN B 87 ASN E 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21648 Z= 0.203 Angle : 0.605 11.412 29296 Z= 0.285 Chirality : 0.035 0.121 3184 Planarity : 0.003 0.042 3840 Dihedral : 3.563 38.023 2956 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.13 % Allowed : 25.27 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.17), residues: 2640 helix: 3.71 (0.12), residues: 1776 sheet: 2.30 (0.49), residues: 156 loop : -0.65 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.004 0.000 HIS E 237 PHE 0.012 0.001 PHE G 181 TYR 0.016 0.001 TYR A 123 ARG 0.010 0.000 ARG H 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASN cc_start: 0.8519 (m110) cc_final: 0.8113 (m-40) REVERT: H 301 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7342 (mmp80) REVERT: H 335 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6700 (mp) REVERT: A 81 ASN cc_start: 0.8518 (m110) cc_final: 0.8128 (m-40) REVERT: A 155 ARG cc_start: 0.8863 (mtm-85) cc_final: 0.8416 (mpp80) REVERT: B 301 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7343 (mmp80) REVERT: B 335 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6701 (mp) REVERT: D 81 ASN cc_start: 0.8519 (m110) cc_final: 0.8121 (m-40) REVERT: D 155 ARG cc_start: 0.8939 (mpp80) cc_final: 0.8642 (mpp80) REVERT: E 301 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7349 (mmp80) REVERT: E 335 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6701 (mp) REVERT: F 81 ASN cc_start: 0.8521 (m110) cc_final: 0.8113 (m-40) REVERT: G 301 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7344 (mmp80) REVERT: G 335 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6697 (mp) outliers start: 25 outliers final: 12 residues processed: 189 average time/residue: 1.5128 time to fit residues: 320.7148 Evaluate side-chains 197 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 263 optimal weight: 9.9990 chunk 242 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 166 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21648 Z= 0.203 Angle : 0.616 10.890 29296 Z= 0.292 Chirality : 0.035 0.152 3184 Planarity : 0.003 0.047 3840 Dihedral : 3.556 37.963 2956 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.27 % Allowed : 24.86 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.17), residues: 2640 helix: 3.71 (0.12), residues: 1776 sheet: 2.35 (0.59), residues: 112 loop : -0.58 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.006 0.001 HIS E 237 PHE 0.029 0.001 PHE C 324 TYR 0.016 0.001 TYR D 123 ARG 0.012 0.000 ARG G 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASN cc_start: 0.8512 (m110) cc_final: 0.8130 (m-40) REVERT: C 155 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.8644 (mpp80) REVERT: H 301 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7328 (mmp80) REVERT: H 335 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6736 (mp) REVERT: A 81 ASN cc_start: 0.8509 (m110) cc_final: 0.8126 (m-40) REVERT: A 155 ARG cc_start: 0.8863 (mtm-85) cc_final: 0.8404 (mpp80) REVERT: B 301 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7299 (mmp80) REVERT: B 335 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6737 (mp) REVERT: D 81 ASN cc_start: 0.8506 (m110) cc_final: 0.8108 (m-40) REVERT: E 301 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7342 (mmp80) REVERT: E 335 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6738 (mp) REVERT: F 81 ASN cc_start: 0.8514 (m110) cc_final: 0.8130 (m-40) REVERT: F 155 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8640 (mpp80) REVERT: G 301 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7305 (mmp80) REVERT: G 335 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6709 (mp) outliers start: 28 outliers final: 18 residues processed: 198 average time/residue: 1.5413 time to fit residues: 341.7580 Evaluate side-chains 207 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.3980 chunk 64 optimal weight: 0.3980 chunk 193 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.128775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074187 restraints weight = 34956.717| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.95 r_work: 0.2813 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21648 Z= 0.190 Angle : 0.615 10.836 29296 Z= 0.289 Chirality : 0.035 0.126 3184 Planarity : 0.003 0.052 3840 Dihedral : 3.534 37.580 2956 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.31 % Allowed : 24.77 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.17), residues: 2640 helix: 3.73 (0.12), residues: 1776 sheet: 2.37 (0.50), residues: 156 loop : -0.65 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.004 0.000 HIS E 237 PHE 0.012 0.001 PHE G 181 TYR 0.015 0.001 TYR A 123 ARG 0.014 0.000 ARG E 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7070.98 seconds wall clock time: 125 minutes 58.00 seconds (7558.00 seconds total)