Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 21:23:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/08_2023/8p3p_17389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/08_2023/8p3p_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_17389/08_2023/8p3p_17389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/08_2023/8p3p_17389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/08_2023/8p3p_17389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3p_17389/08_2023/8p3p_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-1.21rc1-5044/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: 10.44, per 1000 atoms: 0.49 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: 10.11 Conformation dependent library (CDL) restraints added in 3.0 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: 1.71 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: 7.00 Time building geometry restraints manager: 10.44 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: 6.410 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: 0.010 Extract box with map and model: 26.590 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 55.560 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.810 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.307 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 outliers start: 19 outliers final: 12 residues processed: 204 average time/residue: 1.6470 time to fit residues: 374.2972 Evaluate side-chains 188 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 2.540 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 3.4568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 239 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.8602 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 21648 Z= 0.283 Angle : 0.556 7.138 29296 Z= 0.275 Chirality : 0.037 0.150 3184 Planarity : 0.003 0.035 3840 Dihedral : 3.523 15.814 2952 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.99 % 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: 3.54 (0.17), residues: 2640 helix: 3.48 (0.12), residues: 1772 sheet: 2.22 (0.58), residues: 112 loop : -0.62 (0.21), residues: 756 *********************** 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: 44 poor density : 182 time to evaluate : 2.745 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 outliers start: 44 outliers final: 21 residues processed: 206 average time/residue: 1.5427 time to fit residues: 356.3738 Evaluate side-chains 206 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 2.357 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 1.3454 time to fit residues: 15.3366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.0030 chunk 74 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 240 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 213 optimal weight: 0.3980 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 0.0030 chunk 192 optimal weight: 1.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- 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: 0.8563 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 21648 Z= 0.151 Angle : 0.515 7.365 29296 Z= 0.251 Chirality : 0.034 0.123 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.353 14.943 2952 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.26 % 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: 3.75 (0.17), residues: 2640 helix: 3.60 (0.12), residues: 1776 sheet: 2.36 (0.49), residues: 156 loop : -0.65 (0.23), residues: 708 *********************** 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 249 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 199 time to evaluate : 2.561 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 outliers start: 50 outliers final: 19 residues processed: 229 average time/residue: 1.6026 time to fit residues: 411.4000 Evaluate side-chains 203 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 1.2423 time to fit residues: 8.9605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 241 optimal weight: 0.5980 chunk 255 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 chunk 228 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8579 moved from start: 0.0820 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= 0.195 Angle : 0.530 7.882 29296 Z= 0.259 Chirality : 0.035 0.154 3184 Planarity : 0.003 0.033 3840 Dihedral : 3.364 15.064 2952 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 3.22 % 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: 3.73 (0.17), residues: 2640 helix: 3.63 (0.12), residues: 1776 sheet: 2.35 (0.58), residues: 112 loop : -0.57 (0.22), residues: 752 *********************** 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 264 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 193 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 outliers start: 71 outliers final: 20 residues processed: 238 average time/residue: 1.4380 time to fit residues: 386.8094 Evaluate side-chains 207 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 2.491 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 1.3363 time to fit residues: 14.3112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 3 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0819 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= 0.216 Angle : 0.547 9.569 29296 Z= 0.264 Chirality : 0.035 0.121 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.417 15.243 2952 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.63 % 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: 3.80 (0.17), residues: 2640 helix: 3.64 (0.12), residues: 1776 sheet: 2.35 (0.49), residues: 156 loop : -0.63 (0.23), residues: 708 *********************** 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 253 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 195 time to evaluate : 2.545 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 outliers start: 58 outliers final: 24 residues processed: 221 average time/residue: 1.6087 time to fit residues: 396.9471 Evaluate side-chains 209 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 2.490 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 15 residues processed: 9 average time/residue: 1.2148 time to fit residues: 15.8127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 255 optimal weight: 0.4980 chunk 212 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN A 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 21648 Z= 0.198 Angle : 0.556 8.753 29296 Z= 0.269 Chirality : 0.035 0.148 3184 Planarity : 0.003 0.035 3840 Dihedral : 3.405 15.095 2952 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 2.90 % 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: 3.66 (0.12), residues: 1776 sheet: 2.38 (0.49), residues: 156 loop : -0.63 (0.23), residues: 708 *********************** 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 260 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 196 time to evaluate : 2.447 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 outliers start: 64 outliers final: 23 residues processed: 229 average time/residue: 1.6000 time to fit residues: 410.1572 Evaluate side-chains 210 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 2.473 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 1.3814 time to fit residues: 9.7290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 142 optimal weight: 0.3980 chunk 254 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 155 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN D 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 21648 Z= 0.163 Angle : 0.558 9.392 29296 Z= 0.265 Chirality : 0.034 0.120 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.338 14.666 2952 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 2.08 % 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: 3.88 (0.17), residues: 2640 helix: 3.71 (0.12), residues: 1776 sheet: 2.47 (0.50), residues: 156 loop : -0.65 (0.23), residues: 708 *********************** 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 242 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 2.607 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 outliers start: 46 outliers final: 27 residues processed: 226 average time/residue: 1.5783 time to fit residues: 399.6047 Evaluate side-chains 206 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 2.437 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 1.2063 time to fit residues: 8.9454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 151 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 30.0000 chunk 200 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN A 270 ASN D 270 ASN ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 21648 Z= 0.299 Angle : 0.614 9.971 29296 Z= 0.295 Chirality : 0.037 0.155 3184 Planarity : 0.004 0.037 3840 Dihedral : 3.531 16.077 2952 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 2.04 % 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: 3.66 (0.12), residues: 1772 sheet: 2.27 (0.49), residues: 160 loop : -0.68 (0.23), residues: 708 *********************** 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 227 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 182 time to evaluate : 2.396 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 outliers start: 45 outliers final: 22 residues processed: 215 average time/residue: 1.5162 time to fit residues: 367.7058 Evaluate side-chains 201 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 1.2123 time to fit residues: 9.0311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.5980 chunk 222 optimal weight: 0.8980 chunk 237 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8579 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 21648 Z= 0.199 Angle : 0.615 11.572 29296 Z= 0.288 Chirality : 0.035 0.120 3184 Planarity : 0.004 0.046 3840 Dihedral : 3.476 15.121 2952 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.40 % 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: 3.85 (0.17), residues: 2640 helix: 3.69 (0.12), residues: 1776 sheet: 2.36 (0.50), residues: 156 loop : -0.64 (0.23), residues: 708 *********************** 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 212 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 2.732 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 outliers start: 31 outliers final: 19 residues processed: 203 average time/residue: 1.5931 time to fit residues: 362.3171 Evaluate side-chains 195 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 2.409 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 1.3941 time to fit residues: 10.0292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 242 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 166 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.004 0.044 21648 Z= 0.233 Angle : 0.638 11.154 29296 Z= 0.301 Chirality : 0.036 0.154 3184 Planarity : 0.004 0.046 3840 Dihedral : 3.500 15.237 2952 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.86 % 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: 2.31 (0.49), residues: 160 loop : -0.67 (0.23), residues: 704 ********************** 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 200 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 2.705 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 outliers start: 19 outliers final: 18 residues processed: 197 average time/residue: 1.6388 time to fit residues: 360.9131 Evaluate side-chains 194 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 1.4471 time to fit residues: 8.3438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.127795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.073024 restraints weight = 34978.908| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.97 r_work: 0.2792 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21648 Z= 0.224 Angle : 0.638 12.140 29296 Z= 0.298 Chirality : 0.036 0.125 3184 Planarity : 0.004 0.052 3840 Dihedral : 3.501 15.197 2952 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.13 % 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: 3.84 (0.17), residues: 2640 helix: 3.67 (0.12), residues: 1776 sheet: 2.45 (0.51), residues: 156 loop : -0.64 (0.23), residues: 708 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7303.87 seconds wall clock time: 130 minutes 39.96 seconds (7839.96 seconds total)