Starting phenix.real_space_refine on Fri Jul 19 10:55:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/07_2024/8sda_40350.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/07_2024/8sda_40350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/07_2024/8sda_40350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/07_2024/8sda_40350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/07_2024/8sda_40350.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/07_2024/8sda_40350.cif" } resolution = 3.32 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= 0.001 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 7 5.49 5 S 36 5.16 5 C 4963 2.51 5 N 1117 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1825 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1823 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1744 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1749 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {' K': 3, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' K': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 5.21, per 1000 atoms: 0.70 Number of scatterers: 7414 At special positions: 0 Unit cell: (96.28, 96.28, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 36 16.00 P 7 15.00 O 1287 8.00 N 1117 7.00 C 4963 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.709A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 4.047A pdb=" N THR A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 removed outlier: 3.682A pdb=" N VAL A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.569A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 276 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 323 through 350 Processing helix chain 'A' and resid 359 through 373 removed outlier: 4.173A pdb=" N TRP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.694A pdb=" N ILE A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.567A pdb=" N ILE A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.521A pdb=" N LYS B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 224 through 247 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.560A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 300 through 308 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 323 through 349 removed outlier: 3.520A pdb=" N LEU B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 372 removed outlier: 4.157A pdb=" N TRP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.735A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 181 through 206 removed outlier: 4.002A pdb=" N THR D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 250 through 256 removed outlier: 3.596A pdb=" N GLY D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 275 Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 289 through 299 Processing helix chain 'D' and resid 300 through 308 Processing helix chain 'D' and resid 310 through 349 removed outlier: 4.220A pdb=" N ARG D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 372 removed outlier: 4.113A pdb=" N TRP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 403 removed outlier: 3.692A pdb=" N ALA D 402 " --> pdb=" O VAL D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 427 removed outlier: 4.368A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 224 through 247 removed outlier: 3.858A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 removed outlier: 4.013A pdb=" N PHE C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 276 removed outlier: 3.740A pdb=" N ILE C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 300 through 308 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.524A pdb=" N GLN C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 349 removed outlier: 3.585A pdb=" N GLY C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 372 removed outlier: 4.116A pdb=" N TRP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 403 Processing helix chain 'C' and resid 403 through 427 removed outlier: 4.594A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1107 1.30 - 1.43: 1874 1.43 - 1.56: 4478 1.56 - 1.68: 26 1.68 - 1.81: 65 Bond restraints: 7550 Sorted by residual: bond pdb=" C21 POV D 602 " pdb=" O21 POV D 602 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 POV A 603 " pdb=" O21 POV A 603 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C21 POV A 604 " pdb=" O21 POV A 604 " ideal model delta sigma weight residual 1.330 1.457 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C31 POV A 606 " pdb=" O31 POV A 606 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 POV C 603 " pdb=" O21 POV C 603 " ideal model delta sigma weight residual 1.330 1.444 -0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 7545 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 199 106.29 - 113.22: 4315 113.22 - 120.15: 2691 120.15 - 127.08: 2956 127.08 - 134.01: 74 Bond angle restraints: 10235 Sorted by residual: angle pdb=" O13 POV A 601 " pdb=" P POV A 601 " pdb=" O14 POV A 601 " ideal model delta sigma weight residual 121.11 108.34 12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" O11 POV A 602 " pdb=" P POV A 602 " pdb=" O12 POV A 602 " ideal model delta sigma weight residual 97.67 109.76 -12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" O13 POV B 602 " pdb=" P POV B 602 " pdb=" O14 POV B 602 " ideal model delta sigma weight residual 121.11 109.07 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV D 601 " pdb=" P POV D 601 " pdb=" O12 POV D 601 " ideal model delta sigma weight residual 97.67 109.48 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 POV C 602 " pdb=" P POV C 602 " pdb=" O12 POV C 602 " ideal model delta sigma weight residual 97.67 109.43 -11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 4212 26.14 - 52.27: 221 52.27 - 78.41: 33 78.41 - 104.54: 9 104.54 - 130.68: 1 Dihedral angle restraints: 4476 sinusoidal: 1731 harmonic: 2745 Sorted by residual: dihedral pdb=" C3 POV A 601 " pdb=" C31 POV A 601 " pdb=" O31 POV A 601 " pdb=" C32 POV A 601 " ideal model delta sinusoidal sigma weight residual 172.61 41.93 130.68 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CB GLU A 239 " pdb=" CG GLU A 239 " pdb=" CD GLU A 239 " pdb=" OE1 GLU A 239 " ideal model delta sinusoidal sigma weight residual 0.00 -83.23 83.23 1 3.00e+01 1.11e-03 9.41e+00 dihedral pdb=" CA GLU B 349 " pdb=" CB GLU B 349 " pdb=" CG GLU B 349 " pdb=" CD GLU B 349 " ideal model delta sinusoidal sigma weight residual 60.00 115.59 -55.59 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 4473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 996 0.051 - 0.103: 215 0.103 - 0.154: 27 0.154 - 0.205: 5 0.205 - 0.257: 2 Chirality restraints: 1245 Sorted by residual: chirality pdb=" CG LEU D 327 " pdb=" CB LEU D 327 " pdb=" CD1 LEU D 327 " pdb=" CD2 LEU D 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU C 225 " pdb=" N LEU C 225 " pdb=" C LEU C 225 " pdb=" CB LEU C 225 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA HIS C 227 " pdb=" N HIS C 227 " pdb=" C HIS C 227 " pdb=" CB HIS C 227 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 1242 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 406 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C PRO B 406 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO B 406 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 407 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 397 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C GLY D 397 " 0.052 2.00e-02 2.50e+03 pdb=" O GLY D 397 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL D 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 207 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 208 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.025 5.00e-02 4.00e+02 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.81: 2086 2.81 - 3.39: 9155 3.39 - 3.97: 13853 3.97 - 4.56: 19809 4.56 - 5.14: 27639 Nonbonded interactions: 72542 Sorted by model distance: nonbonded pdb=" O THR B 319 " pdb=" OG SER B 323 " model vdw 2.225 2.440 nonbonded pdb=" O ILE D 407 " pdb=" ND2 ASN D 411 " model vdw 2.280 2.520 nonbonded pdb=" O TYR A 376 " pdb=" K K A 609 " model vdw 2.320 2.850 nonbonded pdb=" O THR C 372 " pdb=" OG1 THR C 373 " model vdw 2.327 2.440 nonbonded pdb=" O THR A 372 " pdb=" OG1 THR A 373 " model vdw 2.355 2.440 ... (remaining 72537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or \ resid 319 through 321 or (resid 322 and (name N or name CA or name C or name O \ or name CB )) or resid 323 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'B' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 325 or (resid 326 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'C' and (resid 172 through 211 or resid 224 through 228 or (resid 229 thr \ ough 230 and (name N or name CA or name C or name O or name CB )) or resid 231 t \ hrough 273 or (resid 274 and (name N or name CA or name C or name O or name CB ) \ ) or resid 275 or resid 288 through 409 or (resid 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 427)) selection = (chain 'D' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 175 or (resid 176 through 177 and (name N o \ r name CA or name C or name O or name CB )) or resid 178 through 308 or (resid 3 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 310 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 through 427)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.910 Find NCS groups from input model: 0.550 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.008 0.128 7550 Z= 0.507 Angle : 1.113 12.774 10235 Z= 0.501 Chirality : 0.043 0.257 1245 Planarity : 0.005 0.045 1217 Dihedral : 15.987 130.675 2686 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 1.62 (0.29), residues: 915 helix: 1.30 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 0.42 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 172 HIS 0.004 0.001 HIS C 227 PHE 0.011 0.001 PHE A 194 TYR 0.017 0.001 TYR C 416 ARG 0.009 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.846 Fit side-chains REVERT: D 298 MET cc_start: 0.7594 (ttm) cc_final: 0.6911 (tmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2400 time to fit residues: 52.9010 Evaluate side-chains 123 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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: 6.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 309 HIS D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7550 Z= 0.243 Angle : 0.574 8.647 10235 Z= 0.290 Chirality : 0.039 0.136 1245 Planarity : 0.004 0.033 1217 Dihedral : 12.970 108.942 1160 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.17 % Allowed : 11.40 % Favored : 86.43 % 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: 2.36 (0.29), residues: 915 helix: 1.83 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.49 (0.56), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 365 HIS 0.003 0.001 HIS B 309 PHE 0.020 0.001 PHE B 415 TYR 0.019 0.001 TYR D 269 ARG 0.005 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8305 (tp30) cc_final: 0.7842 (tp30) REVERT: B 322 ARG cc_start: 0.8313 (tmm-80) cc_final: 0.7920 (ttp80) REVERT: D 238 MET cc_start: 0.6360 (ttp) cc_final: 0.6158 (tmm) REVERT: D 298 MET cc_start: 0.7566 (ttm) cc_final: 0.6919 (tmm) outliers start: 16 outliers final: 10 residues processed: 162 average time/residue: 0.2242 time to fit residues: 46.8810 Evaluate side-chains 138 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 GLN C 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.205 Angle : 0.511 6.692 10235 Z= 0.260 Chirality : 0.038 0.126 1245 Planarity : 0.004 0.033 1217 Dihedral : 11.745 98.187 1160 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.31 % Allowed : 14.25 % Favored : 83.45 % 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: 2.62 (0.29), residues: 915 helix: 2.01 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.60 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.002 0.000 HIS D 309 PHE 0.013 0.001 PHE B 415 TYR 0.011 0.001 TYR B 269 ARG 0.007 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.859 Fit side-chains REVERT: D 298 MET cc_start: 0.7538 (ttm) cc_final: 0.6914 (tmm) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 0.2287 time to fit residues: 44.1118 Evaluate side-chains 140 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 372 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7550 Z= 0.286 Angle : 0.553 6.826 10235 Z= 0.278 Chirality : 0.039 0.128 1245 Planarity : 0.004 0.050 1217 Dihedral : 11.392 90.874 1160 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.85 % Allowed : 17.10 % Favored : 80.05 % 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: 2.54 (0.29), residues: 915 helix: 1.95 (0.19), residues: 751 sheet: None (None), residues: 0 loop : 0.61 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.003 0.001 HIS D 309 PHE 0.016 0.001 PHE B 274 TYR 0.012 0.001 TYR B 269 ARG 0.006 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.926 Fit side-chains REVERT: A 418 GLU cc_start: 0.8540 (tp30) cc_final: 0.8277 (tp30) REVERT: D 298 MET cc_start: 0.7562 (ttm) cc_final: 0.6945 (tmm) outliers start: 21 outliers final: 15 residues processed: 142 average time/residue: 0.2405 time to fit residues: 43.7382 Evaluate side-chains 139 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 372 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7550 Z= 0.192 Angle : 0.503 6.927 10235 Z= 0.253 Chirality : 0.038 0.124 1245 Planarity : 0.004 0.035 1217 Dihedral : 10.744 88.926 1160 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.44 % Allowed : 17.91 % Favored : 79.65 % 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: 2.76 (0.29), residues: 915 helix: 2.11 (0.19), residues: 751 sheet: None (None), residues: 0 loop : 0.66 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.000 HIS D 309 PHE 0.019 0.001 PHE B 274 TYR 0.011 0.001 TYR B 269 ARG 0.008 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.817 Fit side-chains REVERT: A 418 GLU cc_start: 0.8450 (tp30) cc_final: 0.8161 (tp30) REVERT: B 309 HIS cc_start: 0.8760 (m90) cc_final: 0.8534 (m90) REVERT: D 298 MET cc_start: 0.7557 (ttm) cc_final: 0.6958 (tmm) REVERT: C 238 MET cc_start: 0.6776 (tmm) cc_final: 0.6533 (tmm) REVERT: C 297 ILE cc_start: 0.8426 (mt) cc_final: 0.8093 (mt) outliers start: 18 outliers final: 15 residues processed: 146 average time/residue: 0.2323 time to fit residues: 43.7724 Evaluate side-chains 142 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 372 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7550 Z= 0.162 Angle : 0.499 7.118 10235 Z= 0.249 Chirality : 0.037 0.120 1245 Planarity : 0.004 0.035 1217 Dihedral : 10.071 84.846 1160 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.58 % Allowed : 18.05 % Favored : 79.38 % 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: 2.84 (0.29), residues: 915 helix: 2.15 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.67 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 366 HIS 0.001 0.000 HIS D 309 PHE 0.020 0.001 PHE B 274 TYR 0.009 0.001 TYR B 269 ARG 0.007 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.843 Fit side-chains REVERT: A 418 GLU cc_start: 0.8438 (tp30) cc_final: 0.8156 (tp30) REVERT: B 309 HIS cc_start: 0.8734 (m90) cc_final: 0.8478 (m90) REVERT: D 298 MET cc_start: 0.7545 (ttm) cc_final: 0.6949 (tmm) REVERT: D 301 LEU cc_start: 0.7898 (tp) cc_final: 0.7673 (tp) REVERT: C 238 MET cc_start: 0.6751 (tmm) cc_final: 0.6524 (tmm) REVERT: C 297 ILE cc_start: 0.8426 (mt) cc_final: 0.8099 (mt) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 0.2370 time to fit residues: 45.0295 Evaluate side-chains 142 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 372 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.206 Angle : 0.518 7.265 10235 Z= 0.259 Chirality : 0.038 0.124 1245 Planarity : 0.004 0.035 1217 Dihedral : 9.776 84.758 1160 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.31 % Allowed : 19.67 % Favored : 78.02 % 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: 2.86 (0.28), residues: 915 helix: 2.16 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.70 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 365 HIS 0.002 0.000 HIS D 309 PHE 0.021 0.001 PHE B 274 TYR 0.009 0.001 TYR B 269 ARG 0.008 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.881 Fit side-chains REVERT: A 418 GLU cc_start: 0.8441 (tp30) cc_final: 0.8114 (tp30) REVERT: B 309 HIS cc_start: 0.8738 (m90) cc_final: 0.8466 (m90) REVERT: D 298 MET cc_start: 0.7567 (ttm) cc_final: 0.6967 (tmm) REVERT: C 238 MET cc_start: 0.6771 (tmm) cc_final: 0.6538 (tmm) REVERT: C 297 ILE cc_start: 0.8425 (mt) cc_final: 0.8107 (mt) REVERT: C 352 GLU cc_start: 0.8023 (pp20) cc_final: 0.7494 (pp20) REVERT: C 416 TYR cc_start: 0.7639 (t80) cc_final: 0.7390 (m-80) outliers start: 17 outliers final: 12 residues processed: 140 average time/residue: 0.2330 time to fit residues: 41.8144 Evaluate side-chains 137 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 372 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.193 Angle : 0.513 7.327 10235 Z= 0.257 Chirality : 0.037 0.121 1245 Planarity : 0.004 0.035 1217 Dihedral : 9.538 85.219 1160 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.31 % Allowed : 19.54 % Favored : 78.15 % 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: 2.95 (0.28), residues: 915 helix: 2.20 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.88 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.002 0.000 HIS D 309 PHE 0.023 0.001 PHE B 274 TYR 0.009 0.001 TYR B 269 ARG 0.008 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.793 Fit side-chains REVERT: A 418 GLU cc_start: 0.8451 (tp30) cc_final: 0.8119 (tp30) REVERT: B 309 HIS cc_start: 0.8722 (m90) cc_final: 0.8456 (m90) REVERT: D 298 MET cc_start: 0.7567 (ttm) cc_final: 0.6970 (tmm) REVERT: D 301 LEU cc_start: 0.7810 (tp) cc_final: 0.7591 (tp) REVERT: C 238 MET cc_start: 0.6806 (tmm) cc_final: 0.6569 (tmm) REVERT: C 352 GLU cc_start: 0.8041 (pp20) cc_final: 0.7509 (pp20) outliers start: 17 outliers final: 16 residues processed: 140 average time/residue: 0.2365 time to fit residues: 42.3827 Evaluate side-chains 142 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 372 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.0060 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7550 Z= 0.170 Angle : 0.513 7.645 10235 Z= 0.256 Chirality : 0.037 0.121 1245 Planarity : 0.004 0.035 1217 Dihedral : 9.232 86.075 1160 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.44 % Allowed : 19.54 % Favored : 78.02 % 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: 3.02 (0.29), residues: 915 helix: 2.25 (0.19), residues: 759 sheet: None (None), residues: 0 loop : 0.90 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 365 HIS 0.001 0.000 HIS D 309 PHE 0.025 0.001 PHE B 274 TYR 0.009 0.001 TYR B 269 ARG 0.009 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.876 Fit side-chains REVERT: A 318 PHE cc_start: 0.7925 (t80) cc_final: 0.7596 (m-80) REVERT: A 418 GLU cc_start: 0.8431 (tp30) cc_final: 0.8090 (tp30) REVERT: B 274 PHE cc_start: 0.7868 (t80) cc_final: 0.7641 (t80) REVERT: B 309 HIS cc_start: 0.8709 (m90) cc_final: 0.8496 (m90) REVERT: D 298 MET cc_start: 0.7560 (ttm) cc_final: 0.6970 (tmm) REVERT: C 297 ILE cc_start: 0.8442 (mt) cc_final: 0.8104 (mt) REVERT: C 352 GLU cc_start: 0.8089 (pp20) cc_final: 0.7503 (pp20) outliers start: 18 outliers final: 15 residues processed: 139 average time/residue: 0.2389 time to fit residues: 42.6009 Evaluate side-chains 139 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 372 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7550 Z= 0.187 Angle : 0.541 10.321 10235 Z= 0.266 Chirality : 0.038 0.148 1245 Planarity : 0.004 0.035 1217 Dihedral : 9.119 85.975 1160 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.31 % Allowed : 20.08 % Favored : 77.61 % 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: 3.06 (0.29), residues: 915 helix: 2.25 (0.19), residues: 761 sheet: None (None), residues: 0 loop : 1.04 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 365 HIS 0.001 0.000 HIS D 309 PHE 0.023 0.001 PHE B 274 TYR 0.009 0.001 TYR B 269 ARG 0.009 0.001 ARG C 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.860 Fit side-chains REVERT: A 318 PHE cc_start: 0.7928 (t80) cc_final: 0.7568 (m-80) REVERT: A 418 GLU cc_start: 0.8407 (tp30) cc_final: 0.7974 (tp30) REVERT: A 419 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: A 422 GLN cc_start: 0.8183 (mm110) cc_final: 0.7969 (mm110) REVERT: B 309 HIS cc_start: 0.8704 (m90) cc_final: 0.8432 (m90) REVERT: D 298 MET cc_start: 0.7640 (ttm) cc_final: 0.7080 (tmm) REVERT: C 297 ILE cc_start: 0.8468 (mt) cc_final: 0.8124 (mt) REVERT: C 352 GLU cc_start: 0.8120 (pp20) cc_final: 0.7517 (pp20) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 0.2404 time to fit residues: 41.8121 Evaluate side-chains 141 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 372 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 0.0870 chunk 30 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122931 restraints weight = 9892.309| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.07 r_work: 0.3238 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.172 Angle : 0.531 8.839 10235 Z= 0.262 Chirality : 0.037 0.121 1245 Planarity : 0.004 0.035 1217 Dihedral : 8.879 86.597 1160 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.17 % Allowed : 20.08 % Favored : 77.75 % 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: 3.11 (0.29), residues: 915 helix: 2.28 (0.19), residues: 761 sheet: None (None), residues: 0 loop : 1.07 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 365 HIS 0.001 0.000 HIS D 309 PHE 0.009 0.001 PHE A 341 TYR 0.009 0.001 TYR B 269 ARG 0.009 0.001 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.03 seconds wall clock time: 33 minutes 45.56 seconds (2025.56 seconds total)