Starting phenix.real_space_refine on Tue Sep 24 08:45:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2024/8djm_27461.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2024/8djm_27461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2024/8djm_27461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2024/8djm_27461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2024/8djm_27461.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2024/8djm_27461.cif" } resolution = 3.23 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= 0.002 sd= 0.081 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 36 5.16 5 C 4601 2.51 5 N 1114 2.21 5 O 1281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1871 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 3 Chain: "B" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2152 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain breaks: 2 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 944 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 214 Unusual residues: {'AJP': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'AJP': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 5.07, per 1000 atoms: 0.72 Number of scatterers: 7032 At special positions: 0 Unit cell: (113.67, 101.04, 106.934, 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 36 16.00 O 1281 8.00 N 1114 7.00 C 4601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.95 Conformation dependent library (CDL) restraints added in 857.6 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 67.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 0 through 16 Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.689A pdb=" N VAL A 20 " --> pdb=" O HIS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 85 removed outlier: 3.734A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 113 removed outlier: 4.281A pdb=" N LEU A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.700A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.712A pdb=" N ALA A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 181 removed outlier: 4.468A pdb=" N ARG A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Proline residue: A 166 - end of helix removed outlier: 3.568A pdb=" N ASP A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 187 through 223 removed outlier: 3.572A pdb=" N CYS A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 235 through 247 removed outlier: 4.716A pdb=" N VAL A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 273 removed outlier: 3.759A pdb=" N MET A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.979A pdb=" N ALA B 52 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 77 removed outlier: 4.615A pdb=" N THR B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 80 through 106 removed outlier: 3.720A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 153 removed outlier: 4.021A pdb=" N VAL B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.300A pdb=" N TYR B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 3.852A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 212 through 218 removed outlier: 4.016A pdb=" N VAL B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.539A pdb=" N GLU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 253 through 279 Proline residue: B 268 - end of helix removed outlier: 3.527A pdb=" N THR B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 310 through 330 Processing helix chain 'C' and resid 265 through 286 Processing helix chain 'C' and resid 288 through 309 removed outlier: 4.255A pdb=" N VAL C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 removed outlier: 3.713A pdb=" N GLU C 315 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 Processing helix chain 'C' and resid 350 through 367 Processing helix chain 'C' and resid 367 through 383 removed outlier: 4.023A pdb=" N SER C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 382 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.094A pdb=" N ILE L 102 " --> pdb=" O SER L 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.863A pdb=" N LYS H 84 " --> pdb=" O GLN H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 109 Processing sheet with id=AA1, first strand: chain 'L' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'L' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'L' and resid 72 through 73 removed outlier: 6.803A pdb=" N TRP L 54 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA5, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.493A pdb=" N GLU H 29 " --> pdb=" O THR H 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.940A pdb=" N SER H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER H 59 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR H 128 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1188 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: 1.89 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.20: 12 1.20 - 1.40: 2776 1.40 - 1.60: 4287 1.60 - 1.81: 110 1.81 - 2.01: 21 Bond restraints: 7206 Sorted by residual: bond pdb=" C07 AJP B 402 " pdb=" C08 AJP B 402 " ideal model delta sigma weight residual 1.550 2.008 -0.458 2.00e-02 2.50e+03 5.25e+02 bond pdb=" C07 AJP A 405 " pdb=" C08 AJP A 405 " ideal model delta sigma weight residual 1.550 2.003 -0.453 2.00e-02 2.50e+03 5.13e+02 bond pdb=" C01 AJP B 402 " pdb=" C02 AJP B 402 " ideal model delta sigma weight residual 1.521 1.959 -0.438 2.00e-02 2.50e+03 4.79e+02 bond pdb=" C01 AJP A 405 " pdb=" C02 AJP A 405 " ideal model delta sigma weight residual 1.521 1.954 -0.433 2.00e-02 2.50e+03 4.69e+02 bond pdb=" C02 AJP A 405 " pdb=" C03 AJP A 405 " ideal model delta sigma weight residual 1.525 1.103 0.422 2.00e-02 2.50e+03 4.44e+02 ... (remaining 7201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 9687 4.64 - 9.27: 128 9.27 - 13.91: 11 13.91 - 18.54: 3 18.54 - 23.18: 3 Bond angle restraints: 9832 Sorted by residual: angle pdb=" C TRP L 113 " pdb=" CA TRP L 113 " pdb=" CB TRP L 113 " ideal model delta sigma weight residual 108.68 85.50 23.18 1.39e+00 5.18e-01 2.78e+02 angle pdb=" C SER L 26 " pdb=" N PRO L 27 " pdb=" CA PRO L 27 " ideal model delta sigma weight residual 120.51 104.02 16.49 1.26e+00 6.30e-01 1.71e+02 angle pdb=" N SER L 26 " pdb=" CA SER L 26 " pdb=" C SER L 26 " ideal model delta sigma weight residual 109.81 128.99 -19.18 2.21e+00 2.05e-01 7.53e+01 angle pdb=" N PRO L 27 " pdb=" CA PRO L 27 " pdb=" C PRO L 27 " ideal model delta sigma weight residual 112.01 100.76 11.25 1.84e+00 2.95e-01 3.74e+01 angle pdb=" N ILE C 368 " pdb=" CA ILE C 368 " pdb=" C ILE C 368 " ideal model delta sigma weight residual 110.23 116.10 -5.87 1.04e+00 9.25e-01 3.18e+01 ... (remaining 9827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 4395 35.59 - 71.19: 206 71.19 - 106.78: 112 106.78 - 142.37: 70 142.37 - 177.96: 21 Dihedral angle restraints: 4804 sinusoidal: 2311 harmonic: 2493 Sorted by residual: dihedral pdb=" C TRP L 113 " pdb=" N TRP L 113 " pdb=" CA TRP L 113 " pdb=" CB TRP L 113 " ideal model delta harmonic sigma weight residual -122.60 -95.39 -27.21 0 2.50e+00 1.60e-01 1.18e+02 dihedral pdb=" N SER L 26 " pdb=" C SER L 26 " pdb=" CA SER L 26 " pdb=" CB SER L 26 " ideal model delta harmonic sigma weight residual 122.80 138.69 -15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" C SER L 26 " pdb=" N SER L 26 " pdb=" CA SER L 26 " pdb=" CB SER L 26 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.148: 1124 1.148 - 2.295: 0 2.295 - 3.443: 0 3.443 - 4.590: 5 4.590 - 5.738: 46 Chirality restraints: 1175 Sorted by residual: chirality pdb=" C20 AJP A 405 " pdb=" C15 AJP A 405 " pdb=" C19 AJP A 405 " pdb=" C21 AJP A 405 " both_signs ideal model delta sigma weight residual False 2.96 -2.78 5.74 2.00e-01 2.50e+01 8.23e+02 chirality pdb=" C20 AJP B 402 " pdb=" C15 AJP B 402 " pdb=" C19 AJP B 402 " pdb=" C21 AJP B 402 " both_signs ideal model delta sigma weight residual False 2.96 -2.76 5.72 2.00e-01 2.50e+01 8.18e+02 chirality pdb=" C16 AJP A 405 " pdb=" C11 AJP A 405 " pdb=" C15 AJP A 405 " pdb=" C17 AJP A 405 " both_signs ideal model delta sigma weight residual False -2.70 2.87 -5.57 2.00e-01 2.50e+01 7.75e+02 ... (remaining 1172 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP L 113 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C TRP L 113 " 0.044 2.00e-02 2.50e+03 pdb=" O TRP L 113 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO L 114 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 367 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C TYR C 367 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR C 367 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE C 368 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO L 27 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C PRO L 27 " -0.028 2.00e-02 2.50e+03 pdb=" O PRO L 27 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA L 28 " 0.010 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 8 2.45 - 3.07: 3841 3.07 - 3.68: 10424 3.68 - 4.29: 14629 4.29 - 4.90: 25443 Nonbonded interactions: 54345 Sorted by model distance: nonbonded pdb=" N PRO B 309 " pdb=" O VAL C 383 " model vdw 1.844 3.120 nonbonded pdb=" CA PRO B 309 " pdb=" O VAL C 383 " model vdw 2.320 3.470 nonbonded pdb=" C04 AJP A 405 " pdb=" C85 AJP A 405 " model vdw 2.408 3.072 nonbonded pdb=" C04 AJP B 402 " pdb=" C85 AJP B 402 " model vdw 2.416 3.072 nonbonded pdb=" C03 AJP B 402 " pdb=" O84 AJP B 402 " model vdw 2.440 2.752 ... (remaining 54340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.770 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 0.029 0.458 7206 Z= 1.974 Angle : 1.526 23.179 9832 Z= 0.875 Chirality : 1.041 5.738 1175 Planarity : 0.004 0.038 1172 Dihedral : 32.650 177.962 3192 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.82 % Allowed : 3.70 % Favored : 95.47 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 3.23 % 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: -2.26 (0.25), residues: 842 helix: -0.85 (0.19), residues: 501 sheet: -3.36 (0.36), residues: 110 loop : -1.49 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.004 0.001 HIS B 95 PHE 0.014 0.002 PHE B 256 TYR 0.014 0.002 TYR B 150 ARG 0.004 0.001 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.7901 (mmm) cc_final: 0.7561 (tpp) REVERT: B 325 PHE cc_start: 0.7150 (m-10) cc_final: 0.6946 (m-10) REVERT: C 342 LEU cc_start: 0.8466 (tt) cc_final: 0.8213 (pp) REVERT: L 43 ARG cc_start: 0.7443 (ttp-170) cc_final: 0.6648 (ttm-80) REVERT: H 42 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7645 (tttp) REVERT: H 51 TYR cc_start: 0.8871 (m-80) cc_final: 0.8591 (m-80) REVERT: H 86 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7294 (ptpt) REVERT: H 88 THR cc_start: 0.7242 (p) cc_final: 0.6880 (p) REVERT: H 101 GLU cc_start: 0.7664 (tt0) cc_final: 0.7253 (tt0) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.2284 time to fit residues: 29.3644 Evaluate side-chains 82 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 95 HIS B 316 ASN C 272 ASN C 277 ASN C 279 ASN C 337 GLN C 380 GLN L 25 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7206 Z= 0.206 Angle : 1.408 34.630 9832 Z= 0.511 Chirality : 0.138 2.092 1175 Planarity : 0.004 0.035 1172 Dihedral : 23.357 179.620 1675 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.37 % Allowed : 7.82 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.29), residues: 842 helix: 1.44 (0.23), residues: 504 sheet: -2.15 (0.40), residues: 124 loop : -1.03 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 273 HIS 0.002 0.001 HIS A 16 PHE 0.011 0.001 PHE B 180 TYR 0.013 0.001 TYR B 174 ARG 0.002 0.000 ARG L 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7303 (mp) REVERT: A 218 LEU cc_start: 0.7587 (tp) cc_final: 0.7378 (mp) REVERT: B 74 ARG cc_start: 0.6961 (tpm170) cc_final: 0.6760 (mmp80) REVERT: B 151 TYR cc_start: 0.7552 (t80) cc_final: 0.7309 (t80) REVERT: C 342 LEU cc_start: 0.8455 (tt) cc_final: 0.8231 (pp) REVERT: L 43 ARG cc_start: 0.6859 (ttp-170) cc_final: 0.6143 (ttm-80) REVERT: H 42 LYS cc_start: 0.7456 (ttpt) cc_final: 0.6934 (tttm) REVERT: H 51 TYR cc_start: 0.9070 (m-80) cc_final: 0.8808 (m-80) REVERT: H 86 LYS cc_start: 0.7488 (ptpt) cc_final: 0.7174 (ptpt) REVERT: H 101 GLU cc_start: 0.7463 (tt0) cc_final: 0.7225 (tt0) outliers start: 10 outliers final: 9 residues processed: 97 average time/residue: 0.2052 time to fit residues: 27.0385 Evaluate side-chains 93 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 68 optimal weight: 0.0000 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7206 Z= 0.167 Angle : 1.331 33.596 9832 Z= 0.478 Chirality : 0.136 2.001 1175 Planarity : 0.004 0.033 1172 Dihedral : 22.898 178.901 1673 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.51 % Allowed : 8.64 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.03 (0.30), residues: 842 helix: 1.96 (0.23), residues: 505 sheet: -1.57 (0.45), residues: 122 loop : -0.95 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 273 HIS 0.002 0.000 HIS B 278 PHE 0.009 0.001 PHE B 213 TYR 0.015 0.001 TYR H 79 ARG 0.005 0.000 ARG C 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6855 (mtt) cc_final: 0.6562 (tmm) REVERT: A 100 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7344 (mp) REVERT: A 152 GLU cc_start: 0.6711 (tp30) cc_final: 0.6388 (tp30) REVERT: B 151 TYR cc_start: 0.7581 (t80) cc_final: 0.7348 (t80) REVERT: C 342 LEU cc_start: 0.8418 (tt) cc_final: 0.8192 (pp) REVERT: L 43 ARG cc_start: 0.6723 (ttp-170) cc_final: 0.5972 (ttm-80) REVERT: L 80 ARG cc_start: 0.6789 (ptp-170) cc_final: 0.6540 (ptp-170) REVERT: H 51 TYR cc_start: 0.9040 (m-80) cc_final: 0.8778 (m-80) REVERT: H 86 LYS cc_start: 0.7545 (ptpt) cc_final: 0.7201 (ptpt) REVERT: H 96 ARG cc_start: 0.6633 (mtm-85) cc_final: 0.5946 (mtp85) REVERT: H 101 GLU cc_start: 0.7472 (tt0) cc_final: 0.7258 (tt0) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.1890 time to fit residues: 24.8066 Evaluate side-chains 94 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 0.0030 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7206 Z= 0.174 Angle : 1.330 33.893 9832 Z= 0.477 Chirality : 0.136 2.006 1175 Planarity : 0.004 0.035 1172 Dihedral : 22.582 178.910 1673 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.65 % Allowed : 9.47 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.17 (0.30), residues: 842 helix: 1.97 (0.23), residues: 514 sheet: -1.32 (0.46), residues: 122 loop : -0.88 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 273 HIS 0.002 0.001 HIS B 278 PHE 0.009 0.001 PHE B 213 TYR 0.017 0.001 TYR H 79 ARG 0.002 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.800 Fit side-chains REVERT: A 8 MET cc_start: 0.6888 (mtt) cc_final: 0.6587 (tmm) REVERT: A 100 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7405 (mp) REVERT: A 152 GLU cc_start: 0.6758 (tp30) cc_final: 0.6409 (tp30) REVERT: B 151 TYR cc_start: 0.7555 (t80) cc_final: 0.7319 (t80) REVERT: C 304 LEU cc_start: 0.7987 (tp) cc_final: 0.7706 (mm) REVERT: C 342 LEU cc_start: 0.8345 (tt) cc_final: 0.8126 (pp) REVERT: L 43 ARG cc_start: 0.6670 (ttp-170) cc_final: 0.5909 (ttm-80) REVERT: H 39 MET cc_start: 0.7974 (mtm) cc_final: 0.7754 (ptp) REVERT: H 51 TYR cc_start: 0.9044 (m-80) cc_final: 0.8807 (m-80) REVERT: H 86 LYS cc_start: 0.7569 (ptpt) cc_final: 0.7361 (ptpt) REVERT: H 96 ARG cc_start: 0.6637 (mtm-85) cc_final: 0.5875 (mtp85) REVERT: H 101 GLU cc_start: 0.7478 (tt0) cc_final: 0.7274 (tt0) outliers start: 12 outliers final: 10 residues processed: 99 average time/residue: 0.1879 time to fit residues: 25.3790 Evaluate side-chains 96 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.2980 chunk 46 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7206 Z= 0.149 Angle : 1.317 33.589 9832 Z= 0.470 Chirality : 0.136 2.004 1175 Planarity : 0.004 0.038 1172 Dihedral : 22.394 178.520 1673 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 10.29 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.42 (0.30), residues: 842 helix: 2.13 (0.23), residues: 514 sheet: -1.07 (0.48), residues: 122 loop : -0.77 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 273 HIS 0.001 0.000 HIS B 278 PHE 0.010 0.001 PHE B 213 TYR 0.018 0.001 TYR H 79 ARG 0.002 0.000 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6997 (mtt) cc_final: 0.6640 (tmm) REVERT: A 100 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7450 (mp) REVERT: A 152 GLU cc_start: 0.6700 (tp30) cc_final: 0.6358 (tp30) REVERT: B 151 TYR cc_start: 0.7501 (t80) cc_final: 0.7267 (t80) REVERT: B 174 TYR cc_start: 0.8271 (p90) cc_final: 0.8062 (p90) REVERT: C 273 TRP cc_start: 0.5616 (t-100) cc_final: 0.5401 (t-100) REVERT: C 342 LEU cc_start: 0.8317 (tt) cc_final: 0.8099 (pp) REVERT: L 43 ARG cc_start: 0.6621 (ttp-170) cc_final: 0.5866 (ttm-80) REVERT: H 51 TYR cc_start: 0.9022 (m-80) cc_final: 0.8803 (m-80) REVERT: H 86 LYS cc_start: 0.7583 (ptpt) cc_final: 0.7379 (ptpt) REVERT: H 96 ARG cc_start: 0.6608 (mtm-85) cc_final: 0.6090 (mtp85) REVERT: H 101 GLU cc_start: 0.7472 (tt0) cc_final: 0.7243 (tt0) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.1910 time to fit residues: 25.6076 Evaluate side-chains 96 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7206 Z= 0.153 Angle : 1.318 33.740 9832 Z= 0.470 Chirality : 0.135 2.008 1175 Planarity : 0.003 0.039 1172 Dihedral : 22.295 178.763 1671 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.78 % Allowed : 10.56 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.57 (0.30), residues: 842 helix: 2.23 (0.23), residues: 512 sheet: -0.91 (0.48), residues: 122 loop : -0.70 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 273 HIS 0.002 0.001 HIS H 99 PHE 0.010 0.001 PHE B 213 TYR 0.017 0.001 TYR H 79 ARG 0.002 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6992 (mtt) cc_final: 0.6636 (tmm) REVERT: A 152 GLU cc_start: 0.6667 (tp30) cc_final: 0.6203 (tp30) REVERT: B 151 TYR cc_start: 0.7499 (t80) cc_final: 0.7275 (t80) REVERT: B 290 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6634 (mt) REVERT: C 342 LEU cc_start: 0.8294 (tt) cc_final: 0.8083 (pp) REVERT: C 370 LYS cc_start: 0.5364 (pptt) cc_final: 0.4873 (ptpt) REVERT: L 43 ARG cc_start: 0.6635 (ttp-170) cc_final: 0.5868 (ttm-80) REVERT: H 86 LYS cc_start: 0.7620 (ptpt) cc_final: 0.7406 (ptpt) REVERT: H 96 ARG cc_start: 0.6581 (mtm-85) cc_final: 0.6033 (mtp85) REVERT: H 101 GLU cc_start: 0.7486 (tt0) cc_final: 0.7272 (tt0) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.1986 time to fit residues: 25.1728 Evaluate side-chains 92 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7206 Z= 0.183 Angle : 1.325 33.904 9832 Z= 0.474 Chirality : 0.135 2.006 1175 Planarity : 0.003 0.039 1172 Dihedral : 22.323 179.109 1671 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.78 % Allowed : 11.11 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.54 (0.30), residues: 842 helix: 2.18 (0.23), residues: 512 sheet: -0.97 (0.48), residues: 124 loop : -0.61 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 273 HIS 0.002 0.001 HIS H 99 PHE 0.011 0.001 PHE B 213 TYR 0.018 0.001 TYR H 79 ARG 0.001 0.000 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.7025 (mtt) cc_final: 0.6643 (tmm) REVERT: A 152 GLU cc_start: 0.6753 (tp30) cc_final: 0.6278 (tp30) REVERT: B 151 TYR cc_start: 0.7465 (t80) cc_final: 0.7261 (t80) REVERT: C 342 LEU cc_start: 0.8273 (tt) cc_final: 0.8057 (pp) REVERT: C 370 LYS cc_start: 0.5390 (pptt) cc_final: 0.4767 (ptpt) REVERT: L 29 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8680 (mt) REVERT: L 43 ARG cc_start: 0.6631 (ttp-170) cc_final: 0.5867 (ttm-80) REVERT: H 86 LYS cc_start: 0.7644 (ptpt) cc_final: 0.7096 (ptpt) REVERT: H 96 ARG cc_start: 0.6592 (mtm-85) cc_final: 0.6071 (mtp85) REVERT: H 101 GLU cc_start: 0.7577 (tt0) cc_final: 0.7334 (tt0) outliers start: 13 outliers final: 11 residues processed: 96 average time/residue: 0.1893 time to fit residues: 24.7410 Evaluate side-chains 97 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7206 Z= 0.205 Angle : 1.336 34.004 9832 Z= 0.480 Chirality : 0.135 2.006 1175 Planarity : 0.004 0.039 1172 Dihedral : 22.374 179.391 1671 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.65 % Allowed : 11.52 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.48 (0.30), residues: 842 helix: 2.11 (0.23), residues: 512 sheet: -1.04 (0.47), residues: 124 loop : -0.51 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 273 HIS 0.002 0.001 HIS B 230 PHE 0.012 0.001 PHE B 213 TYR 0.018 0.001 TYR H 79 ARG 0.002 0.000 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.7028 (mtt) cc_final: 0.6682 (tmm) REVERT: A 152 GLU cc_start: 0.6780 (tp30) cc_final: 0.6306 (tp30) REVERT: C 342 LEU cc_start: 0.8248 (tt) cc_final: 0.8024 (pp) REVERT: C 370 LYS cc_start: 0.5288 (pptt) cc_final: 0.4708 (ptpt) REVERT: L 29 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8723 (mt) REVERT: L 43 ARG cc_start: 0.6639 (ttp-170) cc_final: 0.5869 (ttm-80) REVERT: H 86 LYS cc_start: 0.7633 (ptpt) cc_final: 0.7393 (ptpt) REVERT: H 96 ARG cc_start: 0.6613 (mtm-85) cc_final: 0.6085 (mtp85) REVERT: H 101 GLU cc_start: 0.7554 (tt0) cc_final: 0.7307 (tt0) outliers start: 12 outliers final: 10 residues processed: 93 average time/residue: 0.1955 time to fit residues: 24.5187 Evaluate side-chains 92 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.1980 chunk 77 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7206 Z= 0.148 Angle : 1.322 33.464 9832 Z= 0.471 Chirality : 0.136 2.003 1175 Planarity : 0.003 0.040 1172 Dihedral : 22.262 178.433 1671 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.23 % Allowed : 11.93 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.68 (0.30), residues: 842 helix: 2.26 (0.23), residues: 512 sheet: -0.85 (0.48), residues: 122 loop : -0.51 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 273 HIS 0.001 0.000 HIS H 99 PHE 0.010 0.001 PHE B 213 TYR 0.017 0.001 TYR H 79 ARG 0.001 0.000 ARG L 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.7069 (mtt) cc_final: 0.6641 (tmm) REVERT: A 152 GLU cc_start: 0.6701 (tp30) cc_final: 0.6255 (tp30) REVERT: C 342 LEU cc_start: 0.8231 (tt) cc_final: 0.8007 (pp) REVERT: C 370 LYS cc_start: 0.5284 (pptt) cc_final: 0.4680 (ptpt) REVERT: L 29 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8729 (mt) REVERT: L 43 ARG cc_start: 0.6607 (ttp-170) cc_final: 0.5840 (ttm-80) REVERT: H 96 ARG cc_start: 0.6564 (mtm-85) cc_final: 0.6015 (mtp85) REVERT: H 101 GLU cc_start: 0.7480 (tt0) cc_final: 0.7258 (tt0) outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 0.1952 time to fit residues: 24.4492 Evaluate side-chains 91 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7206 Z= 0.219 Angle : 1.341 34.230 9832 Z= 0.483 Chirality : 0.135 2.008 1175 Planarity : 0.004 0.039 1172 Dihedral : 22.376 179.514 1671 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.23 % Allowed : 12.35 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.61 (0.30), residues: 842 helix: 2.25 (0.23), residues: 503 sheet: -0.85 (0.47), residues: 122 loop : -0.55 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 273 HIS 0.004 0.001 HIS H 99 PHE 0.012 0.001 PHE B 213 TYR 0.018 0.001 TYR H 79 ARG 0.001 0.000 ARG H 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.721 Fit side-chains REVERT: A 8 MET cc_start: 0.7029 (mtt) cc_final: 0.6683 (tmm) REVERT: A 152 GLU cc_start: 0.6772 (tp30) cc_final: 0.6296 (tp30) REVERT: C 342 LEU cc_start: 0.8196 (tt) cc_final: 0.7956 (pp) REVERT: L 29 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8726 (mt) REVERT: L 43 ARG cc_start: 0.6634 (ttp-170) cc_final: 0.5856 (ttm-80) REVERT: H 96 ARG cc_start: 0.6590 (mtm-85) cc_final: 0.6062 (mtp85) REVERT: H 101 GLU cc_start: 0.7537 (tt0) cc_final: 0.7301 (tt0) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.1872 time to fit residues: 22.3896 Evaluate side-chains 88 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138173 restraints weight = 7770.826| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.52 r_work: 0.3222 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7206 Z= 0.213 Angle : 1.345 34.040 9832 Z= 0.485 Chirality : 0.135 2.003 1175 Planarity : 0.004 0.039 1172 Dihedral : 22.407 179.428 1671 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.23 % Allowed : 12.62 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.55 (0.30), residues: 842 helix: 2.18 (0.23), residues: 503 sheet: -0.83 (0.47), residues: 122 loop : -0.54 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 273 HIS 0.002 0.001 HIS B 278 PHE 0.012 0.001 PHE B 213 TYR 0.016 0.001 TYR H 79 ARG 0.002 0.000 ARG B 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.24 seconds wall clock time: 33 minutes 28.45 seconds (2008.45 seconds total)