Starting phenix.real_space_refine on Tue Sep 24 00:26:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtt_24688/09_2024/7rtt_24688.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtt_24688/09_2024/7rtt_24688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtt_24688/09_2024/7rtt_24688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtt_24688/09_2024/7rtt_24688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtt_24688/09_2024/7rtt_24688.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtt_24688/09_2024/7rtt_24688.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 50 5.16 5 C 4027 2.51 5 N 1013 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 6268 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3058 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 9, 'TRANS': 386} Chain breaks: 1 Chain: "B" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3053 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 9, 'TRANS': 385} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.50, per 1000 atoms: 0.72 Number of scatterers: 6268 At special positions: 0 Unit cell: (84.138, 70.494, 134.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 50 16.00 O 1176 8.00 N 1013 7.00 C 4027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 367 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 129 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 129 " " NAG F 1 " - " ASN B 352 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 858.5 milliseconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 3.790A pdb=" N LEU A 17 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 72 removed outlier: 3.595A pdb=" N PHE A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 158 removed outlier: 3.625A pdb=" N GLY A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 removed outlier: 3.555A pdb=" N GLN A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 235 removed outlier: 3.672A pdb=" N THR A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 270 removed outlier: 3.668A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 251 " --> pdb=" O CYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.753A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.581A pdb=" N TYR A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.522A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.869A pdb=" N THR A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 340 through 365 removed outlier: 4.006A pdb=" N LEU A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.222A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 410 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'B' and resid 11 through 19 removed outlier: 3.901A pdb=" N LEU B 17 " --> pdb=" O TRP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 73 removed outlier: 3.832A pdb=" N GLY B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 160 removed outlier: 3.615A pdb=" N MET B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 188 removed outlier: 3.801A pdb=" N LEU B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 234 removed outlier: 3.840A pdb=" N LYS B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 240 through 276 removed outlier: 4.112A pdb=" N SER B 244 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 251 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 removed outlier: 3.827A pdb=" N TYR B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 308 through 332 Processing helix chain 'B' and resid 340 through 365 removed outlier: 4.163A pdb=" N GLY B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.748A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 410 523 hydrogen bonds defined for protein. 1569 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: 1.35 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1959 1.34 - 1.46: 1527 1.46 - 1.58: 2836 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 6390 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 6385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 8453 1.63 - 3.26: 193 3.26 - 4.89: 43 4.89 - 6.53: 15 6.53 - 8.16: 2 Bond angle restraints: 8706 Sorted by residual: angle pdb=" C VAL A 30 " pdb=" N ASP A 31 " pdb=" CA ASP A 31 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.74e+00 angle pdb=" CB MET A 118 " pdb=" CG MET A 118 " pdb=" SD MET A 118 " ideal model delta sigma weight residual 112.70 120.86 -8.16 3.00e+00 1.11e-01 7.39e+00 angle pdb=" N GLN A 302 " pdb=" CA GLN A 302 " pdb=" C GLN A 302 " ideal model delta sigma weight residual 110.80 115.75 -4.95 2.13e+00 2.20e-01 5.40e+00 angle pdb=" CA TYR B 207 " pdb=" CB TYR B 207 " pdb=" CG TYR B 207 " ideal model delta sigma weight residual 113.90 117.70 -3.80 1.80e+00 3.09e-01 4.45e+00 angle pdb=" CA GLN A 302 " pdb=" C GLN A 302 " pdb=" N SER A 303 " ideal model delta sigma weight residual 116.84 120.40 -3.56 1.71e+00 3.42e-01 4.33e+00 ... (remaining 8701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 3483 21.69 - 43.38: 315 43.38 - 65.07: 39 65.07 - 86.76: 29 86.76 - 108.45: 33 Dihedral angle restraints: 3899 sinusoidal: 1608 harmonic: 2291 Sorted by residual: dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual -86.00 -167.16 81.16 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CA PHE B 273 " pdb=" C PHE B 273 " pdb=" N CYS B 274 " pdb=" CA CYS B 274 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ARG B 237 " pdb=" C ARG B 237 " pdb=" N SER B 238 " pdb=" CA SER B 238 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 3896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1016 0.077 - 0.153: 61 0.153 - 0.230: 0 0.230 - 0.306: 5 0.306 - 0.383: 1 Chirality restraints: 1083 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 129 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1080 not shown) Planarity restraints: 1063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 20 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO A 21 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 211 " -0.017 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR B 211 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 211 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 211 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 211 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 211 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 211 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 211 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 315 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C PHE A 315 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE A 315 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 316 " 0.010 2.00e-02 2.50e+03 ... (remaining 1060 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1185 2.77 - 3.30: 6518 3.30 - 3.84: 10400 3.84 - 4.37: 10633 4.37 - 4.90: 19086 Nonbonded interactions: 47822 Sorted by model distance: nonbonded pdb=" OH TYR B 41 " pdb=" OD2 ASP B 272 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 170 " pdb=" OE1 GLN B 325 " model vdw 2.263 3.040 nonbonded pdb=" O ILE A 226 " pdb=" OG1 THR A 230 " model vdw 2.290 3.040 nonbonded pdb=" NH1 ARG A 156 " pdb=" OD1 ASP A 343 " model vdw 2.296 3.120 nonbonded pdb=" OG SER B 291 " pdb=" NH2 ARG B 295 " model vdw 2.319 3.120 ... (remaining 47817 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 'A' and (resid 5 through 414 or resid 601)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = chain 'F' } 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 group one per residue 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: 1.670 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.990 Find NCS groups from input model: 0.210 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:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6390 Z= 0.223 Angle : 0.632 8.157 8706 Z= 0.305 Chirality : 0.044 0.383 1083 Planarity : 0.005 0.076 1059 Dihedral : 20.568 108.445 2413 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 2.65 (0.32), residues: 783 helix: 2.38 (0.21), residues: 649 sheet: None (None), residues: 0 loop : -1.55 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 12 HIS 0.005 0.001 HIS A 18 PHE 0.011 0.001 PHE B 395 TYR 0.034 0.002 TYR B 211 ARG 0.003 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.447 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1165 time to fit residues: 10.0088 Evaluate side-chains 50 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6390 Z= 0.184 Angle : 0.584 8.508 8706 Z= 0.279 Chirality : 0.039 0.237 1083 Planarity : 0.004 0.053 1059 Dihedral : 15.290 87.856 1087 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.75 % Allowed : 6.27 % Favored : 92.99 % 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: 3.45 (0.32), residues: 783 helix: 2.95 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -1.42 (0.62), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 13 HIS 0.005 0.001 HIS A 18 PHE 0.012 0.001 PHE B 273 TYR 0.014 0.001 TYR B 211 ARG 0.004 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.629 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1434 time to fit residues: 12.4536 Evaluate side-chains 61 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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: 0.6942 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6390 Z= 0.150 Angle : 0.529 7.295 8706 Z= 0.253 Chirality : 0.038 0.252 1083 Planarity : 0.003 0.041 1059 Dihedral : 11.182 79.231 1087 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.34 % Allowed : 10.60 % Favored : 88.06 % 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: 3.75 (0.32), residues: 783 helix: 3.17 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.65 (0.63), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 13 HIS 0.004 0.001 HIS A 18 PHE 0.014 0.001 PHE A 220 TYR 0.010 0.001 TYR A 211 ARG 0.005 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.649 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.1553 time to fit residues: 13.7369 Evaluate side-chains 59 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.0030 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6390 Z= 0.183 Angle : 0.533 7.709 8706 Z= 0.257 Chirality : 0.038 0.265 1083 Planarity : 0.003 0.034 1059 Dihedral : 9.408 71.474 1087 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.49 % Allowed : 12.84 % Favored : 85.67 % 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: 3.83 (0.32), residues: 783 helix: 3.24 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -1.45 (0.63), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 12 HIS 0.004 0.001 HIS A 18 PHE 0.011 0.001 PHE A 173 TYR 0.009 0.001 TYR B 374 ARG 0.003 0.000 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.657 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.1557 time to fit residues: 14.1387 Evaluate side-chains 61 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6390 Z= 0.173 Angle : 0.522 8.101 8706 Z= 0.253 Chirality : 0.037 0.246 1083 Planarity : 0.003 0.030 1059 Dihedral : 8.400 63.995 1087 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.94 % Allowed : 15.07 % Favored : 82.99 % 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: 3.83 (0.32), residues: 783 helix: 3.25 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.56 (0.62), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 13 HIS 0.004 0.001 HIS A 153 PHE 0.010 0.001 PHE B 273 TYR 0.010 0.001 TYR B 210 ARG 0.003 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.588 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.1339 time to fit residues: 12.5567 Evaluate side-chains 61 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6390 Z= 0.189 Angle : 0.533 8.176 8706 Z= 0.258 Chirality : 0.037 0.221 1083 Planarity : 0.003 0.029 1059 Dihedral : 7.645 59.924 1087 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.79 % Allowed : 16.72 % Favored : 81.49 % 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: 3.76 (0.32), residues: 783 helix: 3.20 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.57 (0.62), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 13 HIS 0.003 0.001 HIS A 18 PHE 0.011 0.001 PHE B 273 TYR 0.010 0.001 TYR B 374 ARG 0.001 0.000 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.635 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.1396 time to fit residues: 12.9900 Evaluate side-chains 63 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.0050 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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: 0.6987 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6390 Z= 0.163 Angle : 0.526 8.011 8706 Z= 0.251 Chirality : 0.036 0.213 1083 Planarity : 0.003 0.031 1059 Dihedral : 6.733 59.753 1087 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.94 % Allowed : 16.87 % Favored : 81.19 % 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: 3.83 (0.32), residues: 783 helix: 3.28 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -1.72 (0.61), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS A 18 PHE 0.009 0.001 PHE B 273 TYR 0.008 0.001 TYR A 374 ARG 0.002 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.609 Fit side-chains REVERT: A 151 GLU cc_start: 0.8078 (pp20) cc_final: 0.7775 (tm-30) outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.1262 time to fit residues: 12.6408 Evaluate side-chains 66 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.0040 chunk 42 optimal weight: 0.5980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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: 0.6995 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6390 Z= 0.171 Angle : 0.543 9.361 8706 Z= 0.258 Chirality : 0.036 0.216 1083 Planarity : 0.003 0.029 1059 Dihedral : 6.297 59.588 1087 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.64 % Allowed : 17.46 % Favored : 80.90 % 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: 3.84 (0.32), residues: 783 helix: 3.29 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -1.67 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 13 HIS 0.003 0.001 HIS A 18 PHE 0.009 0.001 PHE B 273 TYR 0.008 0.001 TYR B 374 ARG 0.003 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.603 Fit side-chains REVERT: B 8 TYR cc_start: 0.7079 (t80) cc_final: 0.6519 (t80) REVERT: B 245 MET cc_start: 0.6632 (tpp) cc_final: 0.6391 (tmm) REVERT: B 292 GLU cc_start: 0.6626 (tp30) cc_final: 0.6422 (tp30) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.1134 time to fit residues: 11.5605 Evaluate side-chains 64 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6390 Z= 0.209 Angle : 0.567 7.769 8706 Z= 0.274 Chirality : 0.038 0.225 1083 Planarity : 0.003 0.033 1059 Dihedral : 5.769 57.236 1087 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.64 % Allowed : 17.16 % Favored : 81.19 % 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: 3.65 (0.32), residues: 783 helix: 3.15 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.75 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 13 HIS 0.004 0.001 HIS B 153 PHE 0.013 0.001 PHE B 273 TYR 0.011 0.001 TYR B 374 ARG 0.002 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.692 Fit side-chains REVERT: B 8 TYR cc_start: 0.7158 (t80) cc_final: 0.6736 (t80) REVERT: B 292 GLU cc_start: 0.6710 (tp30) cc_final: 0.6492 (tp30) REVERT: B 350 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7544 (tp) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.1194 time to fit residues: 12.2841 Evaluate side-chains 65 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6390 Z= 0.210 Angle : 0.563 8.151 8706 Z= 0.271 Chirality : 0.037 0.221 1083 Planarity : 0.003 0.028 1059 Dihedral : 5.550 57.174 1087 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.64 % Allowed : 17.01 % Favored : 81.34 % 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: 3.65 (0.32), residues: 783 helix: 3.15 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.79 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 13 HIS 0.004 0.001 HIS A 22 PHE 0.011 0.001 PHE B 273 TYR 0.014 0.001 TYR B 210 ARG 0.003 0.000 ARG B 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.630 Fit side-chains REVERT: B 8 TYR cc_start: 0.7167 (t80) cc_final: 0.6818 (t80) REVERT: B 350 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7450 (tp) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.1148 time to fit residues: 12.1247 Evaluate side-chains 68 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 41 optimal weight: 0.0770 overall best weight: 0.2294 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.210915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.181662 restraints weight = 7062.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.181661 restraints weight = 8175.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.182835 restraints weight = 7375.925| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6390 Z= 0.140 Angle : 0.515 8.266 8706 Z= 0.249 Chirality : 0.035 0.200 1083 Planarity : 0.003 0.037 1059 Dihedral : 5.191 55.707 1087 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.75 % Allowed : 17.91 % Favored : 81.34 % 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: 3.98 (0.32), residues: 783 helix: 3.39 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.74 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.005 0.001 HIS A 153 PHE 0.013 0.001 PHE A 220 TYR 0.012 0.001 TYR B 210 ARG 0.002 0.000 ARG B 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1221.59 seconds wall clock time: 33 minutes 8.04 seconds (1988.04 seconds total)