Starting phenix.real_space_refine on Wed Feb 14 03:30:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/02_2024/7qvm_14180_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/02_2024/7qvm_14180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/02_2024/7qvm_14180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/02_2024/7qvm_14180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/02_2024/7qvm_14180_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/02_2024/7qvm_14180_updated.pdb" } resolution = 3.25 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= 0.026 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 65 5.16 5 C 5450 2.51 5 N 1438 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R GLU 42": "OE1" <-> "OE2" Residue "R PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 189": "OD1" <-> "OD2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8528 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1662 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "L" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "R" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1994 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 239} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1770 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.92, per 1000 atoms: 0.58 Number of scatterers: 8528 At special positions: 0 Unit cell: (93.093, 122.388, 127.596, 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 65 16.00 O 1575 8.00 N 1438 7.00 C 5450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 33.3% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.754A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.024A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.551A pdb=" N ALA A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 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 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 36 through 64 removed outlier: 4.132A pdb=" N VAL R 60 " --> pdb=" O GLY R 56 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU R 61 " --> pdb=" O ASN R 57 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA R 63 " --> pdb=" O CYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 102 removed outlier: 3.644A pdb=" N VAL R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU R 94 " --> pdb=" O VAL R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 109 through 142 removed outlier: 3.858A pdb=" N THR R 127 " --> pdb=" O MET R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 174 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 210 through 229 Processing helix chain 'R' and resid 271 through 300 Proline residue: R 290 - end of helix Processing helix chain 'R' and resid 309 through 316 removed outlier: 3.795A pdb=" N LEU R 316 " --> pdb=" O ILE R 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 332 Proline residue: R 326 - end of helix Processing helix chain 'R' and resid 334 through 337 No H-bonds generated for 'chain 'R' and resid 334 through 337' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 264 through 270 removed outlier: 3.787A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 38 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'B' and resid 69 through 72 removed outlier: 5.905A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.797A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.158A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.697A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.885A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.778A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 4.107A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.420A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 134 through 136 removed outlier: 7.224A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 386 hydrogen bonds defined for protein. 1104 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: 2.41 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2615 1.34 - 1.46: 1455 1.46 - 1.58: 4547 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8709 Sorted by residual: bond pdb=" C THR S 84 " pdb=" N SER S 85 " ideal model delta sigma weight residual 1.333 1.266 0.066 1.29e-02 6.01e+03 2.65e+01 bond pdb=" N ILE L 3 " pdb=" CA ILE L 3 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.50e+00 bond pdb=" N GLN R 92 " pdb=" CA GLN R 92 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.24e-02 6.50e+03 7.27e+00 bond pdb=" N LEU R 316 " pdb=" CA LEU R 316 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.33e-02 5.65e+03 6.57e+00 bond pdb=" N GLN R 171 " pdb=" CA GLN R 171 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.45e+00 ... (remaining 8704 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.08: 123 105.08 - 112.32: 4465 112.32 - 119.56: 2817 119.56 - 126.79: 4276 126.79 - 134.03: 130 Bond angle restraints: 11811 Sorted by residual: angle pdb=" N TYR L 2 " pdb=" CA TYR L 2 " pdb=" C TYR L 2 " ideal model delta sigma weight residual 113.12 109.08 4.04 1.25e+00 6.40e-01 1.04e+01 angle pdb=" N ASP A 9 " pdb=" CA ASP A 9 " pdb=" C ASP A 9 " ideal model delta sigma weight residual 111.07 107.76 3.31 1.07e+00 8.73e-01 9.59e+00 angle pdb=" C THR S 84 " pdb=" N SER S 85 " pdb=" CA SER S 85 " ideal model delta sigma weight residual 122.63 127.03 -4.40 1.44e+00 4.82e-01 9.32e+00 angle pdb=" N MET A 249 " pdb=" CA MET A 249 " pdb=" C MET A 249 " ideal model delta sigma weight residual 110.97 107.66 3.31 1.09e+00 8.42e-01 9.24e+00 angle pdb=" CA LEU L 8 " pdb=" C LEU L 8 " pdb=" O LEU L 8 " ideal model delta sigma weight residual 121.20 118.17 3.03 1.04e+00 9.25e-01 8.50e+00 ... (remaining 11806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4698 17.96 - 35.92: 387 35.92 - 53.88: 55 53.88 - 71.84: 6 71.84 - 89.80: 6 Dihedral angle restraints: 5152 sinusoidal: 1980 harmonic: 3172 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -171.69 85.69 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 153.07 -60.07 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CA GLN S 82 " pdb=" C GLN S 82 " pdb=" N MET S 83 " pdb=" CA MET S 83 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 895 0.035 - 0.070: 312 0.070 - 0.105: 94 0.105 - 0.140: 41 0.140 - 0.175: 9 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CA GLU G 17 " pdb=" N GLU G 17 " pdb=" C GLU G 17 " pdb=" CB GLU G 17 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA MET A 249 " pdb=" N MET A 249 " pdb=" C MET A 249 " pdb=" CB MET A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA LEU A 250 " pdb=" N LEU A 250 " pdb=" C LEU A 250 " pdb=" CB LEU A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 1348 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 341 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C ASP A 341 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP A 341 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 342 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.005 2.00e-02 2.50e+03 1.30e-02 4.24e+00 pdb=" CG TRP B 82 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.016 2.00e-02 2.50e+03 1.08e-02 2.92e+00 pdb=" CG TRP B 63 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.001 2.00e-02 2.50e+03 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 269 2.70 - 3.25: 8843 3.25 - 3.80: 13911 3.80 - 4.35: 17249 4.35 - 4.90: 29422 Nonbonded interactions: 69694 Sorted by model distance: nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.156 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.184 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.234 2.440 nonbonded pdb=" O ALA B 231 " pdb=" OG1 THR B 243 " model vdw 2.239 2.440 nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.248 2.440 ... (remaining 69689 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.540 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.420 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 0.066 8709 Z= 0.214 Angle : 0.640 6.556 11811 Z= 0.359 Chirality : 0.044 0.175 1351 Planarity : 0.004 0.043 1487 Dihedral : 12.937 89.801 3086 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.22 (0.27), residues: 1068 helix: 1.70 (0.29), residues: 353 sheet: -0.52 (0.32), residues: 241 loop : -0.63 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE S 68 TYR 0.010 0.001 TYR S 178 ARG 0.008 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7167 (p90) cc_final: 0.6950 (p90) REVERT: A 243 ARG cc_start: 0.8750 (ptp-110) cc_final: 0.8291 (ptp-110) REVERT: A 249 MET cc_start: 0.8227 (tpt) cc_final: 0.7991 (tpp) REVERT: B 23 LYS cc_start: 0.9109 (tppt) cc_final: 0.8810 (mtmm) REVERT: B 63 TRP cc_start: 0.7775 (m100) cc_final: 0.7539 (m100) REVERT: B 274 THR cc_start: 0.8341 (m) cc_final: 0.7836 (p) REVERT: G 20 LYS cc_start: 0.8863 (ptpp) cc_final: 0.8490 (pttm) REVERT: G 41 CYS cc_start: 0.7026 (t) cc_final: 0.6759 (t) REVERT: R 42 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8642 (mt-10) REVERT: R 79 LYS cc_start: 0.8214 (tttt) cc_final: 0.7646 (mmmt) REVERT: R 92 GLN cc_start: 0.7935 (tp40) cc_final: 0.7238 (tp-100) REVERT: R 119 GLN cc_start: 0.5790 (mt0) cc_final: 0.5418 (mt0) REVERT: R 275 LYS cc_start: 0.7453 (tttt) cc_final: 0.7212 (tttt) REVERT: S 83 MET cc_start: 0.8025 (tpt) cc_final: 0.7554 (tpt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2389 time to fit residues: 63.8668 Evaluate side-chains 172 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0570 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** R 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8709 Z= 0.165 Angle : 0.561 6.525 11811 Z= 0.284 Chirality : 0.041 0.154 1351 Planarity : 0.004 0.043 1487 Dihedral : 4.073 20.392 1169 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.08 % Allowed : 9.60 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.35 (0.27), residues: 1068 helix: 2.18 (0.28), residues: 351 sheet: -0.75 (0.30), residues: 273 loop : -0.64 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE S 200 TYR 0.013 0.001 TYR S 102 ARG 0.005 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7124 (p90) cc_final: 0.6920 (p90) REVERT: A 243 ARG cc_start: 0.8761 (ptp-110) cc_final: 0.8289 (ptp-110) REVERT: A 246 GLU cc_start: 0.8870 (pt0) cc_final: 0.8630 (pt0) REVERT: A 277 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8637 (mm-30) REVERT: A 305 GLN cc_start: 0.9054 (mt0) cc_final: 0.8515 (tt0) REVERT: B 23 LYS cc_start: 0.9098 (tppt) cc_final: 0.8814 (mtpt) REVERT: B 197 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7923 (mmm160) REVERT: G 18 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8538 (tp-100) REVERT: G 20 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8450 (pttm) REVERT: G 41 CYS cc_start: 0.7003 (t) cc_final: 0.6788 (t) REVERT: R 40 ARG cc_start: 0.8477 (ptt90) cc_final: 0.8118 (ptm-80) REVERT: R 42 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8572 (mt-10) REVERT: R 79 LYS cc_start: 0.8090 (tttt) cc_final: 0.7607 (mmmt) REVERT: R 92 GLN cc_start: 0.8101 (tp40) cc_final: 0.7678 (tp40) REVERT: R 275 LYS cc_start: 0.7400 (tttt) cc_final: 0.7174 (tttt) REVERT: S 13 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7979 (mm-40) REVERT: S 76 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8278 (mtmm) outliers start: 10 outliers final: 7 residues processed: 191 average time/residue: 0.2532 time to fit residues: 62.9313 Evaluate side-chains 168 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 157 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8709 Z= 0.262 Angle : 0.583 12.873 11811 Z= 0.294 Chirality : 0.043 0.249 1351 Planarity : 0.004 0.043 1487 Dihedral : 4.224 22.540 1169 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.83 % Allowed : 14.02 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.47 (0.27), residues: 1068 helix: 2.32 (0.28), residues: 348 sheet: -0.65 (0.31), residues: 254 loop : -0.64 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS B 62 PHE 0.013 0.002 PHE S 200 TYR 0.013 0.001 TYR S 50 ARG 0.003 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7184 (p90) cc_final: 0.6981 (p90) REVERT: A 243 ARG cc_start: 0.8873 (ptp-110) cc_final: 0.8395 (ptp-110) REVERT: G 20 LYS cc_start: 0.8898 (ptpp) cc_final: 0.8298 (pttm) REVERT: R 40 ARG cc_start: 0.8500 (ptt90) cc_final: 0.8063 (ptm-80) REVERT: R 78 MET cc_start: 0.7586 (mtp) cc_final: 0.7327 (ttt) REVERT: R 79 LYS cc_start: 0.8144 (tttt) cc_final: 0.7615 (mmmt) REVERT: R 92 GLN cc_start: 0.8140 (tp40) cc_final: 0.7394 (tp-100) REVERT: R 275 LYS cc_start: 0.7397 (tttt) cc_final: 0.7164 (tttt) REVERT: R 332 PHE cc_start: 0.5397 (t80) cc_final: 0.5087 (t80) outliers start: 17 outliers final: 11 residues processed: 182 average time/residue: 0.2456 time to fit residues: 58.4837 Evaluate side-chains 170 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 300 TRP Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 171 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8709 Z= 0.299 Angle : 0.590 9.920 11811 Z= 0.301 Chirality : 0.043 0.206 1351 Planarity : 0.004 0.042 1487 Dihedral : 4.352 23.581 1169 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.27 % Allowed : 16.50 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.33 (0.27), residues: 1068 helix: 2.21 (0.28), residues: 360 sheet: -0.87 (0.30), residues: 279 loop : -0.68 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.012 0.002 PHE B 199 TYR 0.016 0.001 TYR S 50 ARG 0.004 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ARG cc_start: 0.8936 (ptp-110) cc_final: 0.8480 (ptp-110) REVERT: G 20 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8414 (pttm) REVERT: R 40 ARG cc_start: 0.8545 (ptt90) cc_final: 0.8048 (ptm-80) REVERT: R 78 MET cc_start: 0.7611 (mtp) cc_final: 0.7357 (ttt) REVERT: R 79 LYS cc_start: 0.8161 (tttt) cc_final: 0.7637 (mmmt) REVERT: R 226 LYS cc_start: 0.6620 (tppt) cc_final: 0.6240 (mmtm) REVERT: R 275 LYS cc_start: 0.7425 (tttt) cc_final: 0.7162 (tttt) REVERT: R 332 PHE cc_start: 0.5332 (t80) cc_final: 0.5093 (t80) REVERT: S 219 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8526 (pp30) outliers start: 21 outliers final: 15 residues processed: 177 average time/residue: 0.2454 time to fit residues: 57.0207 Evaluate side-chains 170 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 300 TRP Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 219 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8709 Z= 0.259 Angle : 0.584 8.902 11811 Z= 0.296 Chirality : 0.042 0.187 1351 Planarity : 0.004 0.042 1487 Dihedral : 4.322 23.374 1169 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.91 % Allowed : 17.48 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.37 (0.27), residues: 1068 helix: 2.24 (0.28), residues: 360 sheet: -0.84 (0.30), residues: 279 loop : -0.66 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.018 0.001 PHE S 68 TYR 0.026 0.001 TYR A 303 ARG 0.004 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 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: symmetry clash revert: symmetry clash REVERT: A 243 ARG cc_start: 0.8952 (ptp-110) cc_final: 0.8467 (ptp-110) REVERT: B 63 TRP cc_start: 0.7984 (m100) cc_final: 0.7751 (m100) REVERT: B 118 ASP cc_start: 0.7958 (m-30) cc_final: 0.7757 (m-30) REVERT: R 40 ARG cc_start: 0.8536 (ptt90) cc_final: 0.8063 (ptm-80) REVERT: R 78 MET cc_start: 0.7581 (mtp) cc_final: 0.7314 (ttt) REVERT: R 79 LYS cc_start: 0.8172 (tttt) cc_final: 0.7643 (mmmt) REVERT: R 226 LYS cc_start: 0.6618 (tppt) cc_final: 0.6237 (mmtm) REVERT: R 275 LYS cc_start: 0.7417 (tttt) cc_final: 0.7145 (tttt) REVERT: R 332 PHE cc_start: 0.5245 (t80) cc_final: 0.4996 (t80) REVERT: S 13 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7851 (mm-40) REVERT: S 219 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8418 (pp30) outliers start: 27 outliers final: 19 residues processed: 181 average time/residue: 0.2560 time to fit residues: 60.4161 Evaluate side-chains 174 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 300 TRP Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 219 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8709 Z= 0.172 Angle : 0.558 8.421 11811 Z= 0.283 Chirality : 0.041 0.184 1351 Planarity : 0.003 0.041 1487 Dihedral : 4.154 21.621 1169 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.37 % Allowed : 18.45 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.47 (0.27), residues: 1068 helix: 2.32 (0.28), residues: 358 sheet: -0.75 (0.30), residues: 278 loop : -0.61 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.022 0.001 PHE S 68 TYR 0.027 0.001 TYR A 303 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ARG cc_start: 0.8940 (ptp-110) cc_final: 0.8473 (ptp-110) REVERT: A 309 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: A 322 HIS cc_start: 0.8352 (t70) cc_final: 0.7967 (t-90) REVERT: A 346 MET cc_start: 0.8125 (ttp) cc_final: 0.7736 (ptm) REVERT: G 18 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8255 (tp-100) REVERT: G 20 LYS cc_start: 0.9047 (ptmt) cc_final: 0.8714 (pttm) REVERT: R 40 ARG cc_start: 0.8538 (ptt90) cc_final: 0.8057 (ptm-80) REVERT: R 78 MET cc_start: 0.7552 (mtp) cc_final: 0.7322 (ttt) REVERT: R 79 LYS cc_start: 0.8158 (tttt) cc_final: 0.7623 (mmmt) REVERT: R 92 GLN cc_start: 0.7951 (tp40) cc_final: 0.7276 (tp-100) REVERT: R 226 LYS cc_start: 0.6657 (tppt) cc_final: 0.6265 (mmtm) REVERT: R 275 LYS cc_start: 0.7414 (tttt) cc_final: 0.7134 (tttt) REVERT: R 332 PHE cc_start: 0.5124 (t80) cc_final: 0.4871 (t80) REVERT: S 13 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7882 (mm-40) outliers start: 22 outliers final: 18 residues processed: 186 average time/residue: 0.2490 time to fit residues: 60.7211 Evaluate side-chains 178 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 300 TRP Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 217 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 340 ASN R 230 ASN S 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8709 Z= 0.270 Angle : 0.606 10.300 11811 Z= 0.305 Chirality : 0.043 0.184 1351 Planarity : 0.004 0.040 1487 Dihedral : 4.345 23.166 1169 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.24 % Allowed : 18.77 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.42 (0.27), residues: 1068 helix: 2.28 (0.28), residues: 360 sheet: -0.83 (0.30), residues: 278 loop : -0.62 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 63 HIS 0.003 0.001 HIS A 214 PHE 0.026 0.002 PHE S 68 TYR 0.019 0.001 TYR A 303 ARG 0.009 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ARG cc_start: 0.8941 (ptp-110) cc_final: 0.8524 (ptp-110) REVERT: A 309 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: A 322 HIS cc_start: 0.8423 (t70) cc_final: 0.8080 (t-90) REVERT: A 346 MET cc_start: 0.8151 (ttp) cc_final: 0.7751 (ptm) REVERT: G 20 LYS cc_start: 0.9008 (ptmt) cc_final: 0.8671 (pttm) REVERT: R 40 ARG cc_start: 0.8567 (ptt90) cc_final: 0.8071 (ptm-80) REVERT: R 78 MET cc_start: 0.7562 (mtp) cc_final: 0.7327 (ttt) REVERT: R 79 LYS cc_start: 0.8170 (tttt) cc_final: 0.7645 (mmmt) REVERT: R 92 GLN cc_start: 0.8037 (tp40) cc_final: 0.7341 (tp-100) REVERT: R 226 LYS cc_start: 0.6655 (tppt) cc_final: 0.6277 (mmtm) REVERT: R 275 LYS cc_start: 0.7431 (tttt) cc_final: 0.7142 (tttt) REVERT: R 332 PHE cc_start: 0.5137 (t80) cc_final: 0.4866 (t80) outliers start: 30 outliers final: 21 residues processed: 183 average time/residue: 0.2552 time to fit residues: 61.3995 Evaluate side-chains 177 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 300 TRP Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 217 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 0.0070 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8709 Z= 0.238 Angle : 0.593 8.180 11811 Z= 0.302 Chirality : 0.042 0.185 1351 Planarity : 0.004 0.047 1487 Dihedral : 4.329 23.181 1169 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.70 % Allowed : 20.93 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.40 (0.27), residues: 1068 helix: 2.26 (0.28), residues: 360 sheet: -0.82 (0.30), residues: 278 loop : -0.63 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 63 HIS 0.004 0.001 HIS B 62 PHE 0.027 0.001 PHE S 68 TYR 0.019 0.001 TYR A 303 ARG 0.010 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.035 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: A 243 ARG cc_start: 0.8946 (ptp-110) cc_final: 0.8505 (ptp-110) REVERT: A 309 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: A 346 MET cc_start: 0.8156 (ttp) cc_final: 0.7751 (ptm) REVERT: G 18 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8163 (tp-100) REVERT: G 20 LYS cc_start: 0.9063 (ptmt) cc_final: 0.8722 (pttm) REVERT: R 40 ARG cc_start: 0.8568 (ptt90) cc_final: 0.8061 (ptm-80) REVERT: R 78 MET cc_start: 0.7561 (mtp) cc_final: 0.7332 (ttt) REVERT: R 79 LYS cc_start: 0.8168 (tttt) cc_final: 0.7645 (mmmt) REVERT: R 226 LYS cc_start: 0.6545 (tppt) cc_final: 0.6240 (mmtm) REVERT: R 275 LYS cc_start: 0.7399 (tttt) cc_final: 0.7099 (tttt) REVERT: R 332 PHE cc_start: 0.5069 (t80) cc_final: 0.4816 (t80) REVERT: S 13 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7846 (mm-40) outliers start: 25 outliers final: 22 residues processed: 175 average time/residue: 0.2636 time to fit residues: 60.1482 Evaluate side-chains 178 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 96 GLN Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 300 TRP Chi-restraints excluded: chain R residue 323 CYS Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 217 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0060 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8709 Z= 0.172 Angle : 0.601 13.038 11811 Z= 0.300 Chirality : 0.042 0.205 1351 Planarity : 0.004 0.045 1487 Dihedral : 4.128 22.649 1169 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.27 % Allowed : 21.36 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.49 (0.27), residues: 1068 helix: 2.27 (0.28), residues: 363 sheet: -0.75 (0.30), residues: 278 loop : -0.56 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE S 68 TYR 0.012 0.001 TYR A 303 ARG 0.011 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.027 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: A 243 ARG cc_start: 0.8924 (ptp-110) cc_final: 0.8505 (ptp-110) REVERT: A 309 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: A 346 MET cc_start: 0.8119 (ttp) cc_final: 0.7772 (ptm) REVERT: G 18 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8217 (tp-100) REVERT: G 20 LYS cc_start: 0.8987 (ptmt) cc_final: 0.8650 (pttm) REVERT: R 40 ARG cc_start: 0.8569 (ptt90) cc_final: 0.8148 (ptm-80) REVERT: R 78 MET cc_start: 0.7537 (mtp) cc_final: 0.7317 (ttt) REVERT: R 79 LYS cc_start: 0.8161 (tttt) cc_final: 0.7637 (mmmt) REVERT: R 275 LYS cc_start: 0.7404 (tttt) cc_final: 0.7174 (tttt) REVERT: S 13 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7834 (mm-40) REVERT: S 83 MET cc_start: 0.7286 (tpt) cc_final: 0.6860 (tpt) outliers start: 21 outliers final: 16 residues processed: 176 average time/residue: 0.2611 time to fit residues: 59.9174 Evaluate side-chains 172 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 300 TRP Chi-restraints excluded: chain R residue 323 CYS Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 157 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8709 Z= 0.234 Angle : 0.607 9.057 11811 Z= 0.307 Chirality : 0.043 0.207 1351 Planarity : 0.004 0.054 1487 Dihedral : 4.247 22.314 1169 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.94 % Allowed : 22.33 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.48 (0.27), residues: 1068 helix: 2.20 (0.27), residues: 365 sheet: -0.68 (0.30), residues: 277 loop : -0.58 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 63 HIS 0.004 0.001 HIS B 62 PHE 0.018 0.001 PHE S 68 TYR 0.023 0.001 TYR A 303 ARG 0.011 0.001 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ARG cc_start: 0.8940 (ptp-110) cc_final: 0.8517 (ptp-110) REVERT: A 309 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: A 346 MET cc_start: 0.8144 (ttp) cc_final: 0.7774 (ptm) REVERT: G 13 ARG cc_start: 0.9095 (mtt90) cc_final: 0.8785 (mtt90) REVERT: G 18 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8257 (tp-100) REVERT: G 20 LYS cc_start: 0.9029 (ptmt) cc_final: 0.8686 (pttm) REVERT: R 40 ARG cc_start: 0.8615 (ptt90) cc_final: 0.8122 (ptm-80) REVERT: R 78 MET cc_start: 0.7547 (mtp) cc_final: 0.7324 (ttt) REVERT: R 79 LYS cc_start: 0.8167 (tttt) cc_final: 0.7637 (mmmt) REVERT: R 92 GLN cc_start: 0.7928 (tp40) cc_final: 0.7424 (tp-100) REVERT: R 275 LYS cc_start: 0.7384 (tttt) cc_final: 0.7174 (tttt) REVERT: S 13 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7845 (mm-40) REVERT: S 83 MET cc_start: 0.7317 (tpt) cc_final: 0.6836 (tpt) outliers start: 18 outliers final: 17 residues processed: 166 average time/residue: 0.2533 time to fit residues: 54.5545 Evaluate side-chains 168 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 300 TRP Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 157 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.121678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.086233 restraints weight = 16992.422| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.07 r_work: 0.3290 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8709 Z= 0.204 Angle : 0.604 8.888 11811 Z= 0.305 Chirality : 0.043 0.281 1351 Planarity : 0.004 0.050 1487 Dihedral : 4.222 21.872 1169 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.37 % Allowed : 22.01 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.46 (0.27), residues: 1068 helix: 2.19 (0.28), residues: 365 sheet: -0.69 (0.30), residues: 277 loop : -0.60 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.032 0.001 PHE S 200 TYR 0.010 0.001 TYR S 102 ARG 0.011 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.82 seconds wall clock time: 45 minutes 40.66 seconds (2740.66 seconds total)