Starting phenix.real_space_refine on Tue Feb 13 23:01:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4i_31453/02_2024/7f4i_31453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4i_31453/02_2024/7f4i_31453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4i_31453/02_2024/7f4i_31453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4i_31453/02_2024/7f4i_31453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4i_31453/02_2024/7f4i_31453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4i_31453/02_2024/7f4i_31453_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 55 5.16 5 C 5099 2.51 5 N 1407 2.21 5 O 1469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8031 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "A" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1936 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 963 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2577 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2053 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 74 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'4J2:plan-2': 1, 'NLE:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.56, per 1000 atoms: 0.57 Number of scatterers: 8031 At special positions: 0 Unit cell: (85.68, 128.52, 93.177, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 55 16.00 O 1469 8.00 N 1407 7.00 C 5099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 267 " - pdb=" SG CYS R 273 " distance=2.03 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: 3.05 Conformation dependent library (CDL) restraints added in 1.4 seconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 4J2 U 4 " Number of C-beta restraints generated: 1940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 39.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'G' and resid 11 through 23 removed outlier: 3.543A pdb=" N VAL G 16 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 23 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.993A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 253 through 278 removed outlier: 4.403A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.767A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.961A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'R' and resid 44 through 64 Processing helix chain 'R' and resid 67 through 69 No H-bonds generated for 'chain 'R' and resid 67 through 69' Processing helix chain 'R' and resid 72 through 101 Processing helix chain 'R' and resid 110 through 146 removed outlier: 4.407A pdb=" N GLN R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 No H-bonds generated for 'chain 'R' and resid 152 through 155' Processing helix chain 'R' and resid 158 through 181 Processing helix chain 'R' and resid 186 through 225 Processing helix chain 'R' and resid 238 through 266 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 271 through 298 removed outlier: 5.091A pdb=" N CYS R 275 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS R 278 " --> pdb=" O CYS R 275 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN R 281 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP R 294 " --> pdb=" O ALA R 291 " (cutoff:3.500A) Proline residue: R 295 - end of helix removed outlier: 3.551A pdb=" N TYR R 298 " --> pdb=" O PRO R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 310 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.303A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 3 through 6 Processing sheet with id= C, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.253A pdb=" N THR N 125 " --> pdb=" O VAL N 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.177A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.945A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.895A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.798A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.742A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.618A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.438A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.802A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1065 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: 2.43 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2507 1.34 - 1.47: 2037 1.47 - 1.60: 3568 1.60 - 1.73: 0 1.73 - 1.86: 75 Bond restraints: 8187 Sorted by residual: bond pdb=" C 4J2 U 4 " pdb=" N ARG U 5 " ideal model delta sigma weight residual 1.329 1.455 -0.126 1.40e-02 5.10e+03 8.13e+01 bond pdb=" CA ASN B 340 " pdb=" C ASN B 340 " ideal model delta sigma weight residual 1.521 1.481 0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" CE2 4J2 U 4 " pdb=" CZ1 4J2 U 4 " ideal model delta sigma weight residual 1.419 1.364 0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" CA 4J2 U 4 " pdb=" C 4J2 U 4 " ideal model delta sigma weight residual 1.525 1.476 0.049 2.10e-02 2.27e+03 5.53e+00 bond pdb=" CA SER B 343 " pdb=" CB SER B 343 " ideal model delta sigma weight residual 1.530 1.488 0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 8182 not shown) Histogram of bond angle deviations from ideal: 86.19 - 98.72: 1 98.72 - 111.25: 3133 111.25 - 123.78: 7615 123.78 - 136.31: 341 136.31 - 148.84: 2 Bond angle restraints: 11092 Sorted by residual: angle pdb=" O 4J2 U 4 " pdb=" C 4J2 U 4 " pdb=" N ARG U 5 " ideal model delta sigma weight residual 123.00 86.19 36.81 1.60e+00 3.91e-01 5.29e+02 angle pdb=" CA 4J2 U 4 " pdb=" C 4J2 U 4 " pdb=" N ARG U 5 " ideal model delta sigma weight residual 116.20 148.84 -32.64 2.00e+00 2.50e-01 2.66e+02 angle pdb=" C 4J2 U 4 " pdb=" N ARG U 5 " pdb=" CA ARG U 5 " ideal model delta sigma weight residual 121.70 144.60 -22.90 1.80e+00 3.09e-01 1.62e+02 angle pdb=" C HIS U 3 " pdb=" N 4J2 U 4 " pdb=" CA 4J2 U 4 " ideal model delta sigma weight residual 121.70 103.47 18.23 1.80e+00 3.09e-01 1.03e+02 angle pdb=" O ASN B 340 " pdb=" C ASN B 340 " pdb=" N GLY B 341 " ideal model delta sigma weight residual 123.25 117.60 5.65 1.14e+00 7.69e-01 2.46e+01 ... (remaining 11087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4554 17.65 - 35.30: 272 35.30 - 52.95: 36 52.95 - 70.60: 5 70.60 - 88.25: 6 Dihedral angle restraints: 4873 sinusoidal: 1878 harmonic: 2995 Sorted by residual: dihedral pdb=" CA ILE R 40 " pdb=" C ILE R 40 " pdb=" N SER R 41 " pdb=" CA SER R 41 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" N HIS B 54 " pdb=" CA HIS B 54 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 4870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 757 0.049 - 0.098: 385 0.098 - 0.147: 112 0.147 - 0.196: 20 0.196 - 0.245: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA ARG U 5 " pdb=" N ARG U 5 " pdb=" C ARG U 5 " pdb=" CB ARG U 5 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CB ILE R 144 " pdb=" CA ILE R 144 " pdb=" CG1 ILE R 144 " pdb=" CG2 ILE R 144 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1272 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 340 " -0.043 2.00e-02 2.50e+03 8.29e-02 6.87e+01 pdb=" C ASN B 340 " 0.143 2.00e-02 2.50e+03 pdb=" O ASN B 340 " -0.053 2.00e-02 2.50e+03 pdb=" N GLY B 341 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 4J2 U 4 " 0.045 2.00e-02 2.50e+03 6.37e-02 4.06e+01 pdb=" C 4J2 U 4 " -0.110 2.00e-02 2.50e+03 pdb=" O 4J2 U 4 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG U 5 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS U 3 " -0.030 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C HIS U 3 " 0.099 2.00e-02 2.50e+03 pdb=" O HIS U 3 " -0.035 2.00e-02 2.50e+03 pdb=" N 4J2 U 4 " -0.034 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 332 2.72 - 3.26: 8260 3.26 - 3.81: 12890 3.81 - 4.35: 16855 4.35 - 4.90: 28265 Nonbonded interactions: 66602 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.169 2.440 nonbonded pdb=" OD1 ASN N 84 " pdb=" OG SER N 85 " model vdw 2.227 2.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.360 2.520 nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 247 " model vdw 2.378 2.440 nonbonded pdb=" OE2 GLU R 94 " pdb="CA CA R 501 " model vdw 2.389 2.510 ... (remaining 66597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.420 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: 2.130 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.590 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.126 8187 Z= 0.606 Angle : 1.215 36.806 11092 Z= 0.711 Chirality : 0.060 0.245 1275 Planarity : 0.011 0.147 1406 Dihedral : 11.957 88.253 2930 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1010 helix: -0.05 (0.23), residues: 403 sheet: 0.59 (0.36), residues: 211 loop : -0.80 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.009 TRP B 63 HIS 0.018 0.005 HIS G 44 PHE 0.028 0.005 PHE R 76 TYR 0.038 0.006 TYR B 111 ARG 0.057 0.006 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.921 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: G 17 GLU cc_start: 0.9240 (tp30) cc_final: 0.9038 (tp30) REVERT: G 21 MET cc_start: 0.9286 (mmm) cc_final: 0.8997 (mtp) REVERT: G 38 MET cc_start: 0.9111 (ptt) cc_final: 0.8884 (ptp) REVERT: G 48 ASP cc_start: 0.8694 (t0) cc_final: 0.8479 (t0) REVERT: A 25 MET cc_start: 0.7593 (tmm) cc_final: 0.7387 (tmm) REVERT: A 271 ASN cc_start: 0.9029 (m-40) cc_final: 0.8785 (m110) REVERT: A 330 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8799 (mp0) REVERT: N 18 LEU cc_start: 0.8431 (mt) cc_final: 0.7956 (mp) REVERT: N 46 GLU cc_start: 0.8071 (pt0) cc_final: 0.7626 (pt0) REVERT: N 99 CYS cc_start: 0.8432 (m) cc_final: 0.8101 (m) REVERT: N 124 VAL cc_start: 0.9271 (t) cc_final: 0.8802 (t) REVERT: B 10 GLU cc_start: 0.9498 (tt0) cc_final: 0.9123 (tp30) REVERT: B 15 LYS cc_start: 0.9571 (ttmt) cc_final: 0.9332 (tptp) REVERT: B 43 ILE cc_start: 0.9256 (mm) cc_final: 0.9024 (mt) REVERT: B 156 GLN cc_start: 0.8613 (mt0) cc_final: 0.8386 (mt0) REVERT: B 175 GLN cc_start: 0.8388 (pt0) cc_final: 0.8115 (pt0) REVERT: B 209 LYS cc_start: 0.8686 (mttt) cc_final: 0.8164 (mtmt) REVERT: B 280 LYS cc_start: 0.9311 (ttmm) cc_final: 0.8904 (ttmt) REVERT: B 337 LYS cc_start: 0.8356 (mttt) cc_final: 0.8093 (mttt) REVERT: R 290 ASN cc_start: 0.8101 (t0) cc_final: 0.7788 (t0) REVERT: R 294 ASP cc_start: 0.8734 (m-30) cc_final: 0.8389 (m-30) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2722 time to fit residues: 71.4688 Evaluate side-chains 138 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN N 120 GLN B 259 GLN R 70 HIS R 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8187 Z= 0.182 Angle : 0.596 7.793 11092 Z= 0.316 Chirality : 0.043 0.204 1275 Planarity : 0.004 0.039 1406 Dihedral : 5.011 21.762 1122 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.16 % Allowed : 8.49 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 1010 helix: 1.69 (0.26), residues: 405 sheet: 0.46 (0.34), residues: 217 loop : -0.04 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.003 0.001 HIS R 270 PHE 0.020 0.002 PHE G 61 TYR 0.011 0.001 TYR B 105 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.015 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: G 20 LYS cc_start: 0.9516 (ptmm) cc_final: 0.9105 (ptpp) REVERT: G 21 MET cc_start: 0.9346 (mmm) cc_final: 0.9077 (mmm) REVERT: G 32 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8864 (mmmm) REVERT: A 271 ASN cc_start: 0.9131 (m-40) cc_final: 0.8863 (m110) REVERT: N 34 MET cc_start: 0.7817 (mtp) cc_final: 0.7595 (mtp) REVERT: N 73 ASP cc_start: 0.8240 (t0) cc_final: 0.7956 (t0) REVERT: N 76 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8980 (ptmm) REVERT: N 93 VAL cc_start: 0.9262 (t) cc_final: 0.8870 (p) REVERT: N 120 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8134 (mm110) REVERT: B 280 LYS cc_start: 0.9354 (ttmm) cc_final: 0.9092 (ttmm) REVERT: R 83 SER cc_start: 0.9103 (m) cc_final: 0.8863 (t) REVERT: R 238 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7880 (ttpp) outliers start: 10 outliers final: 3 residues processed: 155 average time/residue: 0.2718 time to fit residues: 53.5970 Evaluate side-chains 137 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 172 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 39 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8187 Z= 0.380 Angle : 0.623 8.347 11092 Z= 0.324 Chirality : 0.044 0.224 1275 Planarity : 0.004 0.029 1406 Dihedral : 4.870 21.733 1122 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.21 % Allowed : 10.58 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 1010 helix: 1.77 (0.26), residues: 410 sheet: 0.16 (0.34), residues: 216 loop : 0.02 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.020 0.002 PHE G 61 TYR 0.013 0.001 TYR R 74 ARG 0.006 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9080 (tp30) cc_final: 0.8299 (tp30) REVERT: G 21 MET cc_start: 0.9340 (mmm) cc_final: 0.8959 (mmm) REVERT: G 32 LYS cc_start: 0.9271 (mmmm) cc_final: 0.9052 (mmmm) REVERT: A 271 ASN cc_start: 0.9072 (m-40) cc_final: 0.8762 (m110) REVERT: A 317 ARG cc_start: 0.8401 (mpp80) cc_final: 0.8101 (mpp80) REVERT: N 34 MET cc_start: 0.8017 (mtp) cc_final: 0.7787 (mtp) REVERT: N 73 ASP cc_start: 0.8382 (t0) cc_final: 0.8094 (t0) REVERT: B 45 MET cc_start: 0.8788 (mtt) cc_final: 0.8463 (mtt) REVERT: B 217 MET cc_start: 0.8181 (ppp) cc_final: 0.7894 (ppp) REVERT: B 280 LYS cc_start: 0.9359 (ttmm) cc_final: 0.9077 (ttmm) REVERT: R 304 GLU cc_start: 0.8492 (pp20) cc_final: 0.8163 (pp20) outliers start: 19 outliers final: 11 residues processed: 149 average time/residue: 0.2696 time to fit residues: 50.9757 Evaluate side-chains 134 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.0050 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN B 88 ASN R 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8187 Z= 0.235 Angle : 0.562 7.918 11092 Z= 0.289 Chirality : 0.041 0.158 1275 Planarity : 0.003 0.027 1406 Dihedral : 4.467 18.366 1122 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.98 % Allowed : 13.26 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1010 helix: 1.91 (0.26), residues: 413 sheet: 0.06 (0.34), residues: 215 loop : -0.02 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.008 0.001 HIS R 70 PHE 0.015 0.001 PHE G 61 TYR 0.011 0.001 TYR B 264 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.9340 (mmm) cc_final: 0.8992 (mmt) REVERT: A 271 ASN cc_start: 0.9041 (m-40) cc_final: 0.8681 (m110) REVERT: N 73 ASP cc_start: 0.8367 (t0) cc_final: 0.8040 (t0) REVERT: N 79 LEU cc_start: 0.9280 (tp) cc_final: 0.8943 (tp) REVERT: N 93 VAL cc_start: 0.9194 (t) cc_final: 0.8754 (p) REVERT: B 217 MET cc_start: 0.8240 (ppp) cc_final: 0.7942 (ppp) REVERT: B 280 LYS cc_start: 0.9321 (ttmm) cc_final: 0.8921 (ttmm) REVERT: R 298 TYR cc_start: 0.8997 (m-80) cc_final: 0.8746 (m-80) outliers start: 17 outliers final: 11 residues processed: 142 average time/residue: 0.2651 time to fit residues: 48.1095 Evaluate side-chains 132 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 244 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8187 Z= 0.396 Angle : 0.618 6.865 11092 Z= 0.319 Chirality : 0.043 0.153 1275 Planarity : 0.004 0.030 1406 Dihedral : 4.618 20.183 1122 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.44 % Allowed : 14.19 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 1010 helix: 1.88 (0.26), residues: 411 sheet: -0.02 (0.34), residues: 214 loop : -0.18 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS R 70 PHE 0.018 0.002 PHE G 61 TYR 0.013 0.001 TYR B 264 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 LYS cc_start: 0.9556 (ptmm) cc_final: 0.9253 (ptpp) REVERT: G 21 MET cc_start: 0.9339 (mmm) cc_final: 0.9011 (mmm) REVERT: A 271 ASN cc_start: 0.9079 (m-40) cc_final: 0.8701 (m110) REVERT: N 34 MET cc_start: 0.8131 (mtp) cc_final: 0.7829 (mtp) REVERT: N 73 ASP cc_start: 0.8431 (t0) cc_final: 0.8124 (t0) REVERT: B 217 MET cc_start: 0.8224 (ppp) cc_final: 0.7960 (ppp) REVERT: B 280 LYS cc_start: 0.9327 (ttmm) cc_final: 0.8793 (ttmm) outliers start: 21 outliers final: 17 residues processed: 134 average time/residue: 0.2558 time to fit residues: 44.1364 Evaluate side-chains 131 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8187 Z= 0.276 Angle : 0.564 7.684 11092 Z= 0.290 Chirality : 0.041 0.149 1275 Planarity : 0.003 0.031 1406 Dihedral : 4.418 18.111 1122 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.44 % Allowed : 14.88 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 1010 helix: 1.99 (0.26), residues: 410 sheet: 0.01 (0.34), residues: 214 loop : -0.17 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS R 70 PHE 0.014 0.001 PHE G 61 TYR 0.011 0.001 TYR B 264 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 LYS cc_start: 0.9560 (ptmm) cc_final: 0.9286 (ptpp) REVERT: G 21 MET cc_start: 0.9350 (mmm) cc_final: 0.9037 (mmm) REVERT: A 271 ASN cc_start: 0.9052 (m-40) cc_final: 0.8652 (m110) REVERT: N 1 GLN cc_start: 0.8826 (tt0) cc_final: 0.8436 (pp30) REVERT: N 34 MET cc_start: 0.8090 (mtp) cc_final: 0.7812 (mtp) REVERT: N 73 ASP cc_start: 0.8486 (t0) cc_final: 0.8184 (t0) REVERT: B 10 GLU cc_start: 0.9521 (tt0) cc_final: 0.9253 (mt-10) REVERT: B 280 LYS cc_start: 0.9302 (ttmm) cc_final: 0.8712 (ttmm) REVERT: R 278 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9185 (mmtp) outliers start: 21 outliers final: 16 residues processed: 138 average time/residue: 0.2512 time to fit residues: 44.7025 Evaluate side-chains 134 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN A 267 GLN A 271 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8187 Z= 0.147 Angle : 0.544 11.874 11092 Z= 0.273 Chirality : 0.040 0.152 1275 Planarity : 0.003 0.030 1406 Dihedral : 4.032 16.585 1122 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.98 % Allowed : 15.70 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.27), residues: 1010 helix: 2.19 (0.26), residues: 412 sheet: 0.21 (0.35), residues: 210 loop : -0.15 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 70 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR R 148 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.9334 (mmm) cc_final: 0.9041 (mmm) REVERT: A 271 ASN cc_start: 0.8919 (m110) cc_final: 0.8566 (m110) REVERT: N 1 GLN cc_start: 0.8787 (tt0) cc_final: 0.8417 (pp30) REVERT: N 32 TYR cc_start: 0.9210 (m-80) cc_final: 0.8863 (m-80) REVERT: N 34 MET cc_start: 0.8025 (mtp) cc_final: 0.7773 (mtp) REVERT: N 73 ASP cc_start: 0.8489 (t0) cc_final: 0.8126 (t0) REVERT: B 10 GLU cc_start: 0.9511 (tt0) cc_final: 0.9183 (mt-10) REVERT: B 209 LYS cc_start: 0.8789 (mttt) cc_final: 0.8337 (mttp) REVERT: B 280 LYS cc_start: 0.9289 (ttmm) cc_final: 0.8929 (ttmm) REVERT: B 292 PHE cc_start: 0.8921 (m-10) cc_final: 0.8578 (m-80) REVERT: R 278 LYS cc_start: 0.9484 (mmmm) cc_final: 0.9191 (mmtp) outliers start: 17 outliers final: 11 residues processed: 148 average time/residue: 0.2633 time to fit residues: 49.7031 Evaluate side-chains 136 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 45 PHE Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8187 Z= 0.312 Angle : 0.607 9.182 11092 Z= 0.310 Chirality : 0.041 0.160 1275 Planarity : 0.004 0.047 1406 Dihedral : 4.279 18.389 1122 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.86 % Allowed : 15.70 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1010 helix: 2.12 (0.26), residues: 410 sheet: 0.07 (0.34), residues: 214 loop : -0.11 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.014 0.001 PHE G 61 TYR 0.015 0.001 TYR B 264 ARG 0.009 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.9329 (mmm) cc_final: 0.9042 (mmm) REVERT: A 271 ASN cc_start: 0.9030 (m110) cc_final: 0.8694 (m110) REVERT: N 1 GLN cc_start: 0.8825 (tt0) cc_final: 0.8429 (pp30) REVERT: N 32 TYR cc_start: 0.9260 (m-80) cc_final: 0.8950 (m-80) REVERT: N 34 MET cc_start: 0.8162 (mtp) cc_final: 0.7842 (mtp) REVERT: N 38 ARG cc_start: 0.8888 (ptt180) cc_final: 0.8235 (ptm-80) REVERT: N 73 ASP cc_start: 0.8500 (t0) cc_final: 0.8156 (t0) REVERT: B 10 GLU cc_start: 0.9493 (tt0) cc_final: 0.9250 (mt-10) REVERT: B 280 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8867 (ttmm) REVERT: R 238 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8174 (tttp) REVERT: R 278 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9109 (mmtp) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.2750 time to fit residues: 46.8575 Evaluate side-chains 131 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8187 Z= 0.214 Angle : 0.585 8.840 11092 Z= 0.297 Chirality : 0.040 0.155 1275 Planarity : 0.003 0.034 1406 Dihedral : 4.114 16.617 1122 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.86 % Allowed : 16.16 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1010 helix: 2.25 (0.26), residues: 408 sheet: 0.19 (0.34), residues: 209 loop : -0.09 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR B 264 ARG 0.009 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.9339 (mmm) cc_final: 0.9038 (mmm) REVERT: A 271 ASN cc_start: 0.8972 (m110) cc_final: 0.8622 (m110) REVERT: N 1 GLN cc_start: 0.8824 (tt0) cc_final: 0.8421 (pp30) REVERT: N 32 TYR cc_start: 0.9190 (m-80) cc_final: 0.8928 (m-80) REVERT: N 34 MET cc_start: 0.8060 (mtp) cc_final: 0.7779 (mtp) REVERT: N 38 ARG cc_start: 0.8855 (ptt180) cc_final: 0.8220 (ptm-80) REVERT: N 73 ASP cc_start: 0.8494 (t0) cc_final: 0.8150 (t0) REVERT: N 99 CYS cc_start: 0.8833 (m) cc_final: 0.8226 (m) REVERT: B 10 GLU cc_start: 0.9492 (tt0) cc_final: 0.9232 (mt-10) REVERT: B 209 LYS cc_start: 0.8778 (mttt) cc_final: 0.8357 (mttp) REVERT: B 217 MET cc_start: 0.8301 (ppp) cc_final: 0.7879 (ppp) REVERT: B 280 LYS cc_start: 0.9245 (ttmm) cc_final: 0.8873 (ttmm) REVERT: B 292 PHE cc_start: 0.8996 (m-10) cc_final: 0.8670 (m-80) REVERT: R 73 MET cc_start: 0.7556 (tpt) cc_final: 0.7354 (tpt) REVERT: R 238 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8195 (tttp) REVERT: R 278 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9080 (mmtp) outliers start: 16 outliers final: 14 residues processed: 140 average time/residue: 0.2662 time to fit residues: 47.8881 Evaluate side-chains 135 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 45 PHE Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8187 Z= 0.164 Angle : 0.564 8.399 11092 Z= 0.283 Chirality : 0.040 0.149 1275 Planarity : 0.003 0.033 1406 Dihedral : 3.930 15.950 1122 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.63 % Allowed : 15.93 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1010 helix: 2.44 (0.26), residues: 407 sheet: 0.26 (0.34), residues: 209 loop : -0.15 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR N 95 ARG 0.010 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.9347 (mmm) cc_final: 0.9050 (mmm) REVERT: A 271 ASN cc_start: 0.8927 (m110) cc_final: 0.8580 (m110) REVERT: N 1 GLN cc_start: 0.8825 (tt0) cc_final: 0.8498 (pp30) REVERT: N 32 TYR cc_start: 0.9147 (m-80) cc_final: 0.8840 (m-80) REVERT: N 34 MET cc_start: 0.7946 (mtp) cc_final: 0.7649 (mtp) REVERT: N 38 ARG cc_start: 0.8825 (ptt180) cc_final: 0.8222 (ptm-80) REVERT: N 39 GLN cc_start: 0.8999 (tt0) cc_final: 0.8387 (tm-30) REVERT: N 73 ASP cc_start: 0.8525 (t0) cc_final: 0.8232 (t0) REVERT: N 99 CYS cc_start: 0.8840 (m) cc_final: 0.8198 (m) REVERT: B 10 GLU cc_start: 0.9488 (tt0) cc_final: 0.9262 (mt-10) REVERT: B 209 LYS cc_start: 0.8809 (mttt) cc_final: 0.8292 (mttp) REVERT: B 217 MET cc_start: 0.8329 (ppp) cc_final: 0.7907 (ppp) REVERT: B 280 LYS cc_start: 0.9242 (ttmm) cc_final: 0.8884 (ttmm) REVERT: B 292 PHE cc_start: 0.8856 (m-10) cc_final: 0.8464 (m-80) REVERT: R 238 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8188 (tttp) REVERT: R 278 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9144 (mmtp) outliers start: 14 outliers final: 13 residues processed: 139 average time/residue: 0.2887 time to fit residues: 51.4644 Evaluate side-chains 139 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 45 PHE Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 0.0370 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN B 259 GLN ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060410 restraints weight = 20794.203| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.58 r_work: 0.2834 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8187 Z= 0.194 Angle : 0.572 8.522 11092 Z= 0.287 Chirality : 0.040 0.152 1275 Planarity : 0.003 0.041 1406 Dihedral : 3.949 16.004 1122 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.51 % Allowed : 16.16 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 1010 helix: 2.45 (0.26), residues: 406 sheet: 0.29 (0.34), residues: 209 loop : -0.19 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR N 95 ARG 0.009 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2025.80 seconds wall clock time: 37 minutes 32.54 seconds (2252.54 seconds total)