Starting phenix.real_space_refine on Sat Aug 3 17:06:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6j_36920/08_2024/8k6j_36920.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6j_36920/08_2024/8k6j_36920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6j_36920/08_2024/8k6j_36920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6j_36920/08_2024/8k6j_36920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6j_36920/08_2024/8k6j_36920.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6j_36920/08_2024/8k6j_36920.cif" } resolution = 2.77 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= 0.001 sd= 0.014 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 Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5408 2.51 5 N 1482 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 540": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8580 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4154 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 502} Chain: "B" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1069 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 388} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1690 SG CYS A 216 51.847 62.208 31.752 1.00139.41 S ATOM 1759 SG CYS A 226 52.396 63.171 35.919 1.00104.53 S ATOM 1730 SG CYS A 222 53.627 67.396 32.557 1.00124.35 S ATOM 1690 SG CYS A 216 51.847 62.208 31.752 1.00139.41 S Time building chain proxies: 5.88, per 1000 atoms: 0.69 Number of scatterers: 8580 At special positions: 0 Unit cell: (103.2, 105.78, 78.26, 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) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1636 8.00 N 1482 7.00 C 5408 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " Number of angles added : 9 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 42.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.756A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.849A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.563A pdb=" N LEU A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.056A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.315A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.724A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.668A pdb=" N THR A 513 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.996A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.688A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.589A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.840A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.794A pdb=" N LEU C 450 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.823A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.823A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.718A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.308A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLN A 332 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU A 466 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.199A pdb=" N ASN A 320 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 482 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 385 through 388 removed outlier: 3.659A pdb=" N ARG C 386 " --> pdb=" O ILE C 393 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 909 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: 2.46 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.78: 8724 1.78 - 2.33: 86 2.33 - 2.89: 0 2.89 - 3.44: 0 3.44 - 4.00: 3 Bond restraints: 8813 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.999 -1.699 2.00e-02 2.50e+03 7.22e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.895 -1.637 2.00e-02 2.50e+03 6.70e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.498 -1.265 2.00e-02 2.50e+03 4.00e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 8808 not shown) Histogram of bond angle deviations from ideal: 36.85 - 64.59: 6 64.59 - 92.32: 18 92.32 - 120.06: 7977 120.06 - 147.80: 4042 147.80 - 175.53: 6 Bond angle restraints: 12049 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 63.18 51.57 3.00e+00 1.11e-01 2.96e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 61.43 41.83 3.00e+00 1.11e-01 1.94e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 72.86 39.73 3.00e+00 1.11e-01 1.75e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 36.85 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 39.57 32.18 3.00e+00 1.11e-01 1.15e+02 ... (remaining 12044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4487 17.89 - 35.78: 512 35.78 - 53.68: 148 53.68 - 71.57: 52 71.57 - 89.46: 12 Dihedral angle restraints: 5211 sinusoidal: 2065 harmonic: 3146 Sorted by residual: dihedral pdb=" CA THR A 164 " pdb=" C THR A 164 " pdb=" N PRO A 165 " pdb=" CA PRO A 165 " ideal model delta harmonic sigma weight residual -180.00 -141.86 -38.14 0 5.00e+00 4.00e-02 5.82e+01 dihedral pdb=" CA LEU C 394 " pdb=" C LEU C 394 " pdb=" N MET C 395 " pdb=" CA MET C 395 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ILE B 159 " pdb=" C ILE B 159 " pdb=" N PRO B 160 " pdb=" CA PRO B 160 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 5208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.482: 1274 3.482 - 6.965: 0 6.965 - 10.447: 0 10.447 - 13.929: 0 13.929 - 17.412: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.64 17.41 2.00e-01 2.50e+01 7.58e+03 chirality pdb=" CA PRO A 165 " pdb=" N PRO A 165 " pdb=" C PRO A 165 " pdb=" CB PRO A 165 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1272 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 503 " 0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" CGD HEC C 503 " -0.068 2.00e-02 2.50e+03 pdb=" O1D HEC C 503 " 0.024 2.00e-02 2.50e+03 pdb=" O2D HEC C 503 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 115 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO C 116 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CBA HEC C 503 " 0.014 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" CGA HEC C 503 " -0.051 2.00e-02 2.50e+03 pdb=" O1A HEC C 503 " 0.019 2.00e-02 2.50e+03 pdb=" O2A HEC C 503 " 0.019 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 241 2.68 - 3.24: 8423 3.24 - 3.79: 14759 3.79 - 4.35: 19691 4.35 - 4.90: 32317 Nonbonded interactions: 75431 Sorted by model distance: nonbonded pdb=" OG1 THR A 107 " pdb=" O2A FAD A 601 " model vdw 2.130 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.199 3.040 nonbonded pdb=" N GLU B 136 " pdb=" OE1 GLU B 136 " model vdw 2.204 3.120 nonbonded pdb=" N GLU C 129 " pdb=" OE1 GLU C 129 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP A 63 " pdb=" OG1 THR A 66 " model vdw 2.222 3.040 ... (remaining 75426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.470 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.030 1.699 8813 Z= 1.612 Angle : 1.260 51.573 12049 Z= 0.471 Chirality : 0.490 17.412 1275 Planarity : 0.005 0.076 1564 Dihedral : 17.758 89.459 3203 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.49 % Allowed : 23.22 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1081 helix: 1.88 (0.28), residues: 368 sheet: 0.10 (0.61), residues: 81 loop : -0.09 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 PHE 0.029 0.001 PHE C 156 TYR 0.014 0.001 TYR A 210 ARG 0.014 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7754 (m-40) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 1.2503 time to fit residues: 144.3229 Evaluate side-chains 107 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 8813 Z= 0.310 Angle : 1.037 79.607 12049 Z= 0.397 Chirality : 0.067 1.806 1275 Planarity : 0.005 0.058 1564 Dihedral : 9.841 89.457 1310 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.62 % Allowed : 19.93 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1081 helix: 1.85 (0.28), residues: 387 sheet: -0.23 (0.60), residues: 83 loop : -0.19 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 51 HIS 0.004 0.001 HIS A 409 PHE 0.013 0.001 PHE C 156 TYR 0.008 0.001 TYR A 232 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8950 (p) REVERT: B 136 GLU cc_start: 0.8008 (mp0) cc_final: 0.7742 (mp0) REVERT: B 145 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 267 MET cc_start: 0.9153 (tpt) cc_final: 0.8115 (tpt) outliers start: 32 outliers final: 16 residues processed: 118 average time/residue: 1.2170 time to fit residues: 153.4652 Evaluate side-chains 104 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 56 GLN C 89 HIS C 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 8813 Z= 0.383 Angle : 1.075 82.744 12049 Z= 0.413 Chirality : 0.062 1.504 1275 Planarity : 0.005 0.054 1564 Dihedral : 9.632 89.372 1295 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.74 % Allowed : 20.61 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1081 helix: 1.78 (0.28), residues: 389 sheet: -0.53 (0.59), residues: 83 loop : -0.26 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.004 0.001 HIS A 76 PHE 0.022 0.001 PHE A 80 TYR 0.013 0.001 TYR A 210 ARG 0.007 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8961 (p) REVERT: A 175 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8181 (mtt) REVERT: B 136 GLU cc_start: 0.8062 (mp0) cc_final: 0.7759 (mp0) REVERT: B 145 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: C 267 MET cc_start: 0.9242 (tpt) cc_final: 0.7753 (tpt) REVERT: C 437 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7799 (tp40) REVERT: C 443 LYS cc_start: 0.8479 (mmpt) cc_final: 0.7671 (mttp) outliers start: 33 outliers final: 17 residues processed: 112 average time/residue: 1.1749 time to fit residues: 141.0174 Evaluate side-chains 105 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 437 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8813 Z= 0.221 Angle : 1.029 83.041 12049 Z= 0.390 Chirality : 0.060 1.481 1275 Planarity : 0.004 0.051 1564 Dihedral : 9.285 88.965 1294 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.40 % Allowed : 21.06 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1081 helix: 2.01 (0.28), residues: 381 sheet: -0.55 (0.59), residues: 83 loop : -0.23 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.002 0.000 HIS A 278 PHE 0.012 0.001 PHE A 270 TYR 0.009 0.001 TYR A 443 ARG 0.007 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8956 (p) REVERT: A 175 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7957 (mtt) REVERT: A 192 SER cc_start: 0.8810 (p) cc_final: 0.8590 (p) REVERT: A 211 ASP cc_start: 0.8650 (t0) cc_final: 0.7719 (t0) REVERT: B 91 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8718 (mppt) REVERT: B 136 GLU cc_start: 0.8075 (mp0) cc_final: 0.7780 (mp0) REVERT: C 267 MET cc_start: 0.9269 (tpt) cc_final: 0.7724 (tpt) REVERT: C 395 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8223 (tpt) REVERT: C 443 LYS cc_start: 0.8458 (mmpt) cc_final: 0.7667 (mttp) outliers start: 30 outliers final: 12 residues processed: 115 average time/residue: 1.1949 time to fit residues: 147.0034 Evaluate side-chains 105 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8813 Z= 0.295 Angle : 1.047 83.065 12049 Z= 0.398 Chirality : 0.061 1.500 1275 Planarity : 0.005 0.055 1564 Dihedral : 9.292 89.634 1294 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.28 % Allowed : 21.74 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1081 helix: 1.88 (0.28), residues: 388 sheet: -0.60 (0.59), residues: 83 loop : -0.26 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 PHE 0.021 0.001 PHE C 156 TYR 0.011 0.001 TYR A 210 ARG 0.009 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8972 (p) REVERT: A 175 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8175 (mtt) REVERT: A 211 ASP cc_start: 0.8718 (t0) cc_final: 0.7816 (t0) REVERT: A 462 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: A 514 MET cc_start: 0.9417 (mtp) cc_final: 0.9217 (mtp) REVERT: B 91 LYS cc_start: 0.9220 (mppt) cc_final: 0.8691 (mppt) REVERT: B 136 GLU cc_start: 0.8080 (mp0) cc_final: 0.7742 (mp0) REVERT: B 145 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: C 139 MET cc_start: 0.9045 (mmp) cc_final: 0.8736 (mmp) REVERT: C 395 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8198 (tpt) outliers start: 29 outliers final: 13 residues processed: 108 average time/residue: 1.2355 time to fit residues: 142.7723 Evaluate side-chains 107 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 447 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 56 GLN C 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8813 Z= 0.241 Angle : 1.034 83.084 12049 Z= 0.393 Chirality : 0.060 1.489 1275 Planarity : 0.005 0.053 1564 Dihedral : 9.121 89.725 1293 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.28 % Allowed : 21.97 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1081 helix: 2.04 (0.28), residues: 381 sheet: -0.55 (0.59), residues: 83 loop : -0.24 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 51 HIS 0.002 0.000 HIS A 76 PHE 0.012 0.001 PHE A 270 TYR 0.011 0.001 TYR A 79 ARG 0.011 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8981 (p) REVERT: A 175 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8042 (mtt) REVERT: A 192 SER cc_start: 0.8806 (p) cc_final: 0.8585 (p) REVERT: A 211 ASP cc_start: 0.8727 (t0) cc_final: 0.7838 (t0) REVERT: B 136 GLU cc_start: 0.8100 (mp0) cc_final: 0.7738 (mp0) REVERT: C 139 MET cc_start: 0.9065 (mmp) cc_final: 0.8703 (mmp) REVERT: C 172 ARG cc_start: 0.8817 (mtp85) cc_final: 0.8580 (ptp-110) REVERT: C 395 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8151 (tpt) REVERT: C 443 LYS cc_start: 0.8450 (mmpt) cc_final: 0.7663 (mttp) outliers start: 29 outliers final: 13 residues processed: 110 average time/residue: 1.1921 time to fit residues: 140.3270 Evaluate side-chains 106 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 64 optimal weight: 0.0470 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 56 GLN C 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8813 Z= 0.218 Angle : 1.027 83.051 12049 Z= 0.389 Chirality : 0.060 1.487 1275 Planarity : 0.004 0.051 1564 Dihedral : 8.987 89.641 1293 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.83 % Allowed : 22.76 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1081 helix: 2.08 (0.28), residues: 382 sheet: -0.50 (0.59), residues: 83 loop : -0.23 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.003 0.000 HIS B 64 PHE 0.012 0.001 PHE B 183 TYR 0.018 0.001 TYR A 79 ARG 0.012 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8975 (p) REVERT: A 175 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: A 192 SER cc_start: 0.8775 (p) cc_final: 0.8558 (p) REVERT: A 211 ASP cc_start: 0.8723 (t0) cc_final: 0.7835 (t0) REVERT: A 468 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 505 ASN cc_start: 0.8891 (t0) cc_final: 0.8640 (t160) REVERT: B 86 PHE cc_start: 0.8758 (t80) cc_final: 0.8412 (t80) REVERT: B 91 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8721 (mppt) REVERT: B 136 GLU cc_start: 0.8129 (mp0) cc_final: 0.7758 (mp0) REVERT: C 118 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8463 (mmm) REVERT: C 139 MET cc_start: 0.9069 (mmp) cc_final: 0.8723 (mmp) REVERT: C 267 MET cc_start: 0.9241 (tpt) cc_final: 0.7641 (tpt) REVERT: C 395 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8068 (tpt) REVERT: C 443 LYS cc_start: 0.8434 (mmpt) cc_final: 0.7636 (mttp) outliers start: 25 outliers final: 11 residues processed: 114 average time/residue: 1.2051 time to fit residues: 147.1685 Evaluate side-chains 107 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 447 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8813 Z= 0.237 Angle : 1.047 83.119 12049 Z= 0.397 Chirality : 0.060 1.489 1275 Planarity : 0.005 0.057 1564 Dihedral : 8.899 88.538 1291 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.60 % Allowed : 23.56 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1081 helix: 2.11 (0.28), residues: 382 sheet: -0.47 (0.59), residues: 83 loop : -0.22 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 51 HIS 0.003 0.000 HIS A 76 PHE 0.013 0.001 PHE A 80 TYR 0.015 0.001 TYR A 79 ARG 0.013 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8973 (p) REVERT: A 175 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: A 177 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.8778 (m) REVERT: A 192 SER cc_start: 0.8780 (p) cc_final: 0.8564 (p) REVERT: A 211 ASP cc_start: 0.8723 (t0) cc_final: 0.7769 (t0) REVERT: A 505 ASN cc_start: 0.8876 (t0) cc_final: 0.8587 (t160) REVERT: B 86 PHE cc_start: 0.8762 (t80) cc_final: 0.8512 (t80) REVERT: B 136 GLU cc_start: 0.8121 (mp0) cc_final: 0.7692 (mp0) REVERT: C 139 MET cc_start: 0.9065 (mmp) cc_final: 0.8710 (mmp) REVERT: C 267 MET cc_start: 0.9201 (tpt) cc_final: 0.7518 (tpt) REVERT: C 395 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8026 (tpt) REVERT: C 443 LYS cc_start: 0.8413 (mmpt) cc_final: 0.7618 (mttp) outliers start: 23 outliers final: 12 residues processed: 108 average time/residue: 1.1853 time to fit residues: 137.2271 Evaluate side-chains 105 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 98 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8813 Z= 0.212 Angle : 1.041 83.166 12049 Z= 0.395 Chirality : 0.059 1.479 1275 Planarity : 0.004 0.057 1564 Dihedral : 8.780 87.949 1291 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.15 % Allowed : 24.12 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1081 helix: 2.13 (0.28), residues: 382 sheet: -0.41 (0.60), residues: 83 loop : -0.21 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.002 0.000 HIS B 64 PHE 0.013 0.001 PHE B 183 TYR 0.017 0.001 TYR A 79 ARG 0.013 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 175 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8049 (mtt) REVERT: A 177 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.8794 (m) REVERT: A 211 ASP cc_start: 0.8727 (t0) cc_final: 0.7803 (t0) REVERT: A 468 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7782 (mt-10) REVERT: A 469 MET cc_start: 0.8910 (ttt) cc_final: 0.8598 (tpp) REVERT: A 505 ASN cc_start: 0.8790 (t0) cc_final: 0.7936 (t0) REVERT: B 94 ARG cc_start: 0.8733 (mtm180) cc_final: 0.8341 (mtm180) REVERT: B 136 GLU cc_start: 0.8140 (mp0) cc_final: 0.7760 (mp0) REVERT: C 139 MET cc_start: 0.9063 (mmp) cc_final: 0.8721 (mmp) REVERT: C 267 MET cc_start: 0.9196 (tpt) cc_final: 0.7502 (tpt) REVERT: C 395 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.7976 (ttt) outliers start: 19 outliers final: 8 residues processed: 115 average time/residue: 1.1009 time to fit residues: 136.0530 Evaluate side-chains 105 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 8813 Z= 0.230 Angle : 1.050 83.234 12049 Z= 0.397 Chirality : 0.060 1.481 1275 Planarity : 0.005 0.064 1564 Dihedral : 8.554 87.019 1287 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.70 % Allowed : 24.80 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1081 helix: 2.13 (0.28), residues: 382 sheet: -0.41 (0.60), residues: 83 loop : -0.20 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 128 HIS 0.003 0.000 HIS A 409 PHE 0.024 0.002 PHE C 210 TYR 0.009 0.001 TYR A 210 ARG 0.014 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8976 (p) REVERT: A 175 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8202 (mtt) REVERT: A 211 ASP cc_start: 0.8715 (t0) cc_final: 0.7750 (t0) REVERT: A 276 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: A 468 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7782 (mt-10) REVERT: A 469 MET cc_start: 0.8924 (ttt) cc_final: 0.8606 (tpp) REVERT: A 505 ASN cc_start: 0.8814 (t0) cc_final: 0.8523 (t160) REVERT: B 91 LYS cc_start: 0.9202 (mppt) cc_final: 0.8705 (mppt) REVERT: B 136 GLU cc_start: 0.8146 (mp0) cc_final: 0.7767 (mp0) REVERT: C 139 MET cc_start: 0.9060 (mmp) cc_final: 0.8721 (mmp) REVERT: C 395 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.7915 (tpt) REVERT: C 443 LYS cc_start: 0.8497 (mmpt) cc_final: 0.7638 (mttp) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 1.2251 time to fit residues: 136.3287 Evaluate side-chains 102 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.076432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.060394 restraints weight = 16983.656| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.68 r_work: 0.2622 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 8813 Z= 0.329 Angle : 1.079 83.387 12049 Z= 0.410 Chirality : 0.061 1.500 1275 Planarity : 0.005 0.053 1564 Dihedral : 8.696 87.344 1287 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.93 % Allowed : 24.58 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1081 helix: 1.95 (0.28), residues: 388 sheet: -0.45 (0.60), residues: 83 loop : -0.28 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 PHE 0.029 0.002 PHE B 86 TYR 0.011 0.001 TYR A 210 ARG 0.005 0.000 ARG B 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3084.73 seconds wall clock time: 54 minutes 46.50 seconds (3286.50 seconds total)