Starting phenix.real_space_refine on Thu Nov 14 19:16:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1p_36798/11_2024/8k1p_36798.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1p_36798/11_2024/8k1p_36798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1p_36798/11_2024/8k1p_36798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1p_36798/11_2024/8k1p_36798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1p_36798/11_2024/8k1p_36798.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1p_36798/11_2024/8k1p_36798.cif" } resolution = 3.4 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= 0.064 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 9 5.49 5 Mg 2 5.21 5 S 21 5.16 5 C 4558 2.51 5 N 1240 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7139 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3711 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 20, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain: "C" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1597 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 160 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.91, per 1000 atoms: 0.83 Number of scatterers: 7139 At special positions: 0 Unit cell: (65.6, 87.74, 113.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 21 16.00 P 9 15.00 Mg 2 11.99 O 1308 8.00 N 1240 7.00 C 4558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.40 Conformation dependent library (CDL) restraints added in 977.9 milliseconds 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1652 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 57.8% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.869A pdb=" N LEU A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 48 " --> pdb=" O TRP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.835A pdb=" N GLU A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 3.750A pdb=" N ALA A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.962A pdb=" N LEU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 87 " --> pdb=" O GLN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 105 through 129 removed outlier: 3.514A pdb=" N LEU A 109 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 111 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 4.181A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 168 removed outlier: 3.642A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 199 removed outlier: 3.750A pdb=" N SER A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 228 removed outlier: 3.519A pdb=" N VAL A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.909A pdb=" N TRP A 235 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 276 removed outlier: 3.995A pdb=" N LEU A 258 " --> pdb=" O TRP A 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.598A pdb=" N VAL A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.911A pdb=" N HIS A 331 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 332 " --> pdb=" O VAL A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.350A pdb=" N THR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 437 removed outlier: 3.958A pdb=" N HIS A 409 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 removed outlier: 4.394A pdb=" N THR A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 4.547A pdb=" N LEU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 Proline residue: A 476 - end of helix Processing helix chain 'A' and resid 477 through 496 removed outlier: 4.865A pdb=" N SER A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 540 removed outlier: 3.808A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.515A pdb=" N THR B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.650A pdb=" N ILE B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 removed outlier: 3.890A pdb=" N ALA B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.505A pdb=" N LYS B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 removed outlier: 3.745A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.717A pdb=" N ALA B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.778A pdb=" N ARG C 82 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 111 Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.519A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.667A pdb=" N TYR C 136 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.799A pdb=" N VAL C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 184 Processing helix chain 'C' and resid 194 through 202 removed outlier: 3.561A pdb=" N THR C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 31 removed outlier: 3.550A pdb=" N LEU B 25 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU B 15 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASP B 29 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG B 13 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B 31 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU B 11 " --> pdb=" O THR B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 87 removed outlier: 7.056A pdb=" N ALA B 85 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 157 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 215 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 18 removed outlier: 5.847A pdb=" N LEU C 15 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 37 through 39 removed outlier: 6.209A pdb=" N HIS C 38 " --> pdb=" O LEU C 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 87 removed outlier: 6.829A pdb=" N ALA C 85 " --> pdb=" O LEU C 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.750A pdb=" N VAL C 205 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER C 216 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 207 " --> pdb=" O VAL C 214 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 954 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: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1805 1.33 - 1.48: 2215 1.48 - 1.62: 3204 1.62 - 1.76: 0 1.76 - 1.91: 40 Bond restraints: 7264 Sorted by residual: bond pdb=" C4 ADP B 402 " pdb=" C5 ADP B 402 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5 ADP B 402 " pdb=" C6 ADP B 402 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CA ALA A 281 " pdb=" CB ALA A 281 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.48e-02 4.57e+03 1.27e+01 bond pdb=" CA SER B 49 " pdb=" CB SER B 49 " ideal model delta sigma weight residual 1.532 1.475 0.057 1.62e-02 3.81e+03 1.23e+01 bond pdb=" OB3 CDL A 601 " pdb=" PB2 CDL A 601 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.00e-02 1.00e+04 1.14e+01 ... (remaining 7259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 9767 3.55 - 7.11: 81 7.11 - 10.66: 8 10.66 - 14.21: 2 14.21 - 17.77: 1 Bond angle restraints: 9859 Sorted by residual: angle pdb=" PB ATP C 402 " pdb=" O3B ATP C 402 " pdb=" PG ATP C 402 " ideal model delta sigma weight residual 139.87 122.10 17.77 1.00e+00 1.00e+00 3.16e+02 angle pdb=" N VAL A 60 " pdb=" CA VAL A 60 " pdb=" C VAL A 60 " ideal model delta sigma weight residual 113.71 107.82 5.89 9.50e-01 1.11e+00 3.84e+01 angle pdb=" C ARG A 402 " pdb=" CA ARG A 402 " pdb=" CB ARG A 402 " ideal model delta sigma weight residual 111.22 118.60 -7.38 1.24e+00 6.50e-01 3.54e+01 angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 131.11 5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" N ARG A 402 " pdb=" CA ARG A 402 " pdb=" C ARG A 402 " ideal model delta sigma weight residual 113.20 106.40 6.80 1.36e+00 5.41e-01 2.50e+01 ... (remaining 9854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 4036 25.51 - 51.02: 244 51.02 - 76.53: 46 76.53 - 102.04: 5 102.04 - 127.54: 1 Dihedral angle restraints: 4332 sinusoidal: 1735 harmonic: 2597 Sorted by residual: dihedral pdb=" C5' ADP B 402 " pdb=" O5' ADP B 402 " pdb=" PA ADP B 402 " pdb=" O2A ADP B 402 " ideal model delta sinusoidal sigma weight residual 300.00 172.46 127.54 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" CA CYS B 202 " pdb=" C CYS B 202 " pdb=" N GLU B 203 " pdb=" CA GLU B 203 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA SER C 191 " pdb=" C SER C 191 " pdb=" N SER C 192 " pdb=" CA SER C 192 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 983 0.060 - 0.119: 159 0.119 - 0.179: 17 0.179 - 0.238: 4 0.238 - 0.298: 1 Chirality restraints: 1164 Sorted by residual: chirality pdb=" CA VAL C 59 " pdb=" N VAL C 59 " pdb=" C VAL C 59 " pdb=" CB VAL C 59 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB VAL A 279 " pdb=" CA VAL A 279 " pdb=" CG1 VAL A 279 " pdb=" CG2 VAL A 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA4 CDL A 601 " pdb=" CA3 CDL A 601 " pdb=" CA6 CDL A 601 " pdb=" OA6 CDL A 601 " both_signs ideal model delta sigma weight residual False -2.57 -2.38 -0.19 2.00e-01 2.50e+01 9.19e-01 ... (remaining 1161 not shown) Planarity restraints: 1220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 400 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C VAL A 400 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL A 400 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A 401 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 138 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LYS C 138 " -0.055 2.00e-02 2.50e+03 pdb=" O LYS C 138 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY C 139 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 58 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C LEU C 58 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU C 58 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL C 59 " -0.014 2.00e-02 2.50e+03 ... (remaining 1217 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 59 2.63 - 3.20: 6188 3.20 - 3.76: 10039 3.76 - 4.33: 14156 4.33 - 4.90: 24804 Nonbonded interactions: 55246 Sorted by model distance: nonbonded pdb=" OG SER C 49 " pdb="MG MG C 401 " model vdw 2.062 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2 VO4 B 403 " model vdw 2.127 2.170 nonbonded pdb=" O SER C 163 " pdb=" OG SER C 163 " model vdw 2.301 3.040 nonbonded pdb=" OE2 GLU A 132 " pdb=" NH1 ARG C 53 " model vdw 2.305 3.120 nonbonded pdb=" O ILE B 147 " pdb=" OG SER B 151 " model vdw 2.320 3.040 ... (remaining 55241 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 8 through 219 or resid 401)) selection = (chain 'C' and (resid 8 through 219 or resid 401)) } 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: 4.100 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.540 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.007 0.109 7264 Z= 0.445 Angle : 0.862 17.768 9859 Z= 0.511 Chirality : 0.047 0.298 1164 Planarity : 0.005 0.070 1220 Dihedral : 16.577 127.544 2680 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.27), residues: 926 helix: -0.11 (0.24), residues: 506 sheet: -2.30 (1.17), residues: 23 loop : -2.40 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 44 HIS 0.005 0.001 HIS A 384 PHE 0.022 0.002 PHE C 40 TYR 0.013 0.002 TYR A 64 ARG 0.008 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.775 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.2013 time to fit residues: 24.5886 Evaluate side-chains 75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 27 optimal weight: 0.0470 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7264 Z= 0.196 Angle : 0.583 7.123 9859 Z= 0.291 Chirality : 0.041 0.132 1164 Planarity : 0.004 0.050 1220 Dihedral : 13.792 94.933 1202 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.42 % Allowed : 5.24 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.28), residues: 926 helix: 0.37 (0.24), residues: 520 sheet: -2.12 (1.11), residues: 23 loop : -2.34 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 44 HIS 0.003 0.001 HIS A 404 PHE 0.011 0.001 PHE C 40 TYR 0.015 0.001 TYR A 489 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.778 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 73 average time/residue: 0.2061 time to fit residues: 20.8142 Evaluate side-chains 58 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7264 Z= 0.211 Angle : 0.555 6.402 9859 Z= 0.276 Chirality : 0.041 0.129 1164 Planarity : 0.004 0.048 1220 Dihedral : 12.671 75.596 1202 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.71 % Allowed : 7.93 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 926 helix: 0.58 (0.24), residues: 520 sheet: -1.91 (1.07), residues: 23 loop : -2.27 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 44 HIS 0.003 0.001 HIS A 384 PHE 0.012 0.001 PHE C 40 TYR 0.008 0.001 TYR A 489 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.770 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.2166 time to fit residues: 20.9303 Evaluate side-chains 62 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 216 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.005 0.038 7264 Z= 0.314 Angle : 0.604 6.972 9859 Z= 0.299 Chirality : 0.043 0.134 1164 Planarity : 0.004 0.045 1220 Dihedral : 12.542 74.721 1202 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.13 % Allowed : 10.20 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.28), residues: 926 helix: 0.53 (0.24), residues: 521 sheet: -2.16 (1.03), residues: 23 loop : -2.26 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 44 HIS 0.005 0.001 HIS B 81 PHE 0.012 0.002 PHE C 40 TYR 0.010 0.002 TYR C 86 ARG 0.004 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.762 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 76 average time/residue: 0.1937 time to fit residues: 20.4350 Evaluate side-chains 63 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 216 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7264 Z= 0.213 Angle : 0.545 6.027 9859 Z= 0.273 Chirality : 0.041 0.126 1164 Planarity : 0.004 0.044 1220 Dihedral : 12.020 73.597 1202 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.71 % Allowed : 11.90 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.28), residues: 926 helix: 0.78 (0.24), residues: 515 sheet: -2.27 (0.79), residues: 32 loop : -2.14 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 44 HIS 0.003 0.001 HIS B 81 PHE 0.009 0.001 PHE A 191 TYR 0.007 0.001 TYR C 86 ARG 0.004 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.768 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.1897 time to fit residues: 20.5301 Evaluate side-chains 69 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 193 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7264 Z= 0.186 Angle : 0.532 6.498 9859 Z= 0.264 Chirality : 0.040 0.123 1164 Planarity : 0.004 0.042 1220 Dihedral : 11.734 84.759 1202 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.13 % Allowed : 11.76 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 926 helix: 0.95 (0.24), residues: 516 sheet: -2.10 (0.80), residues: 32 loop : -2.11 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 44 HIS 0.002 0.001 HIS C 38 PHE 0.008 0.001 PHE A 191 TYR 0.012 0.001 TYR A 64 ARG 0.002 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.772 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.1858 time to fit residues: 20.3751 Evaluate side-chains 70 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7264 Z= 0.206 Angle : 0.535 5.966 9859 Z= 0.266 Chirality : 0.040 0.126 1164 Planarity : 0.004 0.048 1220 Dihedral : 11.653 86.096 1202 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.27 % Allowed : 12.32 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.28), residues: 926 helix: 1.03 (0.24), residues: 522 sheet: -1.95 (0.81), residues: 32 loop : -2.14 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 44 HIS 0.003 0.001 HIS B 81 PHE 0.008 0.001 PHE A 191 TYR 0.008 0.001 TYR A 432 ARG 0.002 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.901 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.2110 time to fit residues: 23.1567 Evaluate side-chains 71 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7264 Z= 0.179 Angle : 0.530 7.493 9859 Z= 0.263 Chirality : 0.040 0.125 1164 Planarity : 0.004 0.050 1220 Dihedral : 11.518 89.894 1202 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.99 % Allowed : 13.03 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.28), residues: 926 helix: 1.13 (0.24), residues: 522 sheet: -1.84 (0.82), residues: 32 loop : -2.10 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 44 HIS 0.002 0.001 HIS C 38 PHE 0.008 0.001 PHE A 191 TYR 0.013 0.001 TYR A 64 ARG 0.002 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.657 Fit side-chains REVERT: C 170 MET cc_start: 0.6760 (mmp) cc_final: 0.6519 (mmt) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.1847 time to fit residues: 18.6108 Evaluate side-chains 71 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7264 Z= 0.210 Angle : 0.544 6.771 9859 Z= 0.270 Chirality : 0.040 0.124 1164 Planarity : 0.004 0.051 1220 Dihedral : 11.527 87.816 1202 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.13 % Allowed : 13.31 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.28), residues: 926 helix: 1.14 (0.24), residues: 522 sheet: -1.81 (0.82), residues: 32 loop : -2.08 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 44 HIS 0.003 0.001 HIS C 38 PHE 0.008 0.001 PHE A 191 TYR 0.006 0.001 TYR A 64 ARG 0.002 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.793 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 0.1996 time to fit residues: 19.7892 Evaluate side-chains 71 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 0.0370 chunk 77 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7264 Z= 0.156 Angle : 0.512 6.417 9859 Z= 0.256 Chirality : 0.039 0.122 1164 Planarity : 0.004 0.048 1220 Dihedral : 11.216 84.063 1202 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.85 % Allowed : 13.46 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 926 helix: 1.29 (0.24), residues: 521 sheet: -1.64 (0.82), residues: 32 loop : -2.03 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 44 HIS 0.002 0.001 HIS C 38 PHE 0.008 0.001 PHE A 191 TYR 0.012 0.001 TYR A 64 ARG 0.002 0.000 ARG A 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.720 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.2070 time to fit residues: 20.3107 Evaluate side-chains 67 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.0040 chunk 52 optimal weight: 0.3980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.116995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097984 restraints weight = 8745.284| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.49 r_work: 0.2848 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7264 Z= 0.166 Angle : 0.527 8.628 9859 Z= 0.258 Chirality : 0.039 0.125 1164 Planarity : 0.004 0.049 1220 Dihedral : 11.122 83.729 1202 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.85 % Allowed : 13.60 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 926 helix: 1.35 (0.24), residues: 521 sheet: -1.55 (0.83), residues: 32 loop : -2.02 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 44 HIS 0.002 0.001 HIS C 38 PHE 0.008 0.001 PHE A 191 TYR 0.006 0.001 TYR A 64 ARG 0.002 0.000 ARG C 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1846.48 seconds wall clock time: 34 minutes 17.46 seconds (2057.46 seconds total)