Starting phenix.real_space_refine on Tue Jun 25 19:05:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcn_38248/06_2024/8xcn_38248_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcn_38248/06_2024/8xcn_38248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcn_38248/06_2024/8xcn_38248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcn_38248/06_2024/8xcn_38248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcn_38248/06_2024/8xcn_38248_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcn_38248/06_2024/8xcn_38248_updated.pdb" } resolution = 3.02 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= 0.015 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 5420 2.51 5 N 1489 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C GLU 410": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8601 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4164 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} 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 1767 SG CYS A 226 52.692 62.655 35.511 1.00 87.42 S ATOM 1738 SG CYS A 222 54.833 67.275 31.351 1.00 83.60 S ATOM 1698 SG CYS A 216 52.906 62.684 28.727 1.00 88.54 S Time building chain proxies: 5.40, per 1000 atoms: 0.63 Number of scatterers: 8601 At special positions: 0 Unit cell: (105.78, 107.5, 76.54, 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 1638 8.00 N 1489 7.00 C 5420 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.79 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 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 7 sheets defined 35.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 removed outlier: 3.597A pdb=" N ASN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 139 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 356 through 359 removed outlier: 3.565A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 388 through 401 removed outlier: 3.625A pdb=" N ASP A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 462 removed outlier: 3.521A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 524 through 541 Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 84 through 99 removed outlier: 4.596A pdb=" N SER B 87 " --> pdb=" O HIS B 84 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 88 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 52 through 55 No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 96 through 104 Processing helix chain 'C' and resid 120 through 125 removed outlier: 5.552A pdb=" N ARG C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 201 through 205 removed outlier: 4.070A pdb=" N HIS C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 Processing helix chain 'C' and resid 266 through 273 Processing helix chain 'C' and resid 280 through 290 Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 374 through 382 Processing helix chain 'C' and resid 409 through 422 Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 446 through 450 Processing sheet with id= A, first strand: chain 'A' and resid 506 through 508 removed outlier: 6.754A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS A 247 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 198 through 200 Processing sheet with id= D, first strand: chain 'A' and resid 277 through 281 removed outlier: 3.966A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 326 through 332 Processing sheet with id= F, first strand: chain 'C' and resid 70 through 73 Processing sheet with id= G, first strand: chain 'C' and resid 384 through 388 249 hydrogen bonds defined for protein. 657 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: 2.02 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.57: 8733 1.57 - 2.15: 93 2.15 - 2.74: 6 2.74 - 3.32: 0 3.32 - 3.91: 3 Bond restraints: 8835 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.906 -1.606 2.00e-02 2.50e+03 6.44e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.762 -1.529 2.00e-02 2.50e+03 5.84e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.736 -1.478 2.00e-02 2.50e+03 5.46e+03 bond pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 1.492 0.987 0.505 5.00e-02 4.00e+02 1.02e+02 bond pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 1.503 1.220 0.283 3.40e-02 8.65e+02 6.93e+01 ... (remaining 8830 not shown) Histogram of bond angle deviations from ideal: 38.39 - 66.69: 4 66.69 - 94.98: 26 94.98 - 123.27: 11524 123.27 - 151.56: 517 151.56 - 179.85: 7 Bond angle restraints: 12078 Sorted by residual: angle pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 106.10 179.85 -73.75 3.20e+00 9.77e-02 5.31e+02 angle pdb=" N PRO A 144 " pdb=" CD PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 103.20 76.60 26.60 1.50e+00 4.44e-01 3.14e+02 angle pdb=" CA PRO A 144 " pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 104.50 71.64 32.86 1.90e+00 2.77e-01 2.99e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 68.36 46.39 3.00e+00 1.11e-01 2.39e+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 69.90 42.69 3.00e+00 1.11e-01 2.03e+02 ... (remaining 12073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.37: 4457 19.37 - 38.75: 580 38.75 - 58.12: 146 58.12 - 77.49: 30 77.49 - 96.87: 11 Dihedral angle restraints: 5224 sinusoidal: 2072 harmonic: 3152 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -129.56 -50.44 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" N PRO A 144 " pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " pdb=" CB PRO A 144 " ideal model delta sinusoidal sigma weight residual 30.00 126.87 -96.87 1 1.50e+01 4.44e-03 4.78e+01 dihedral pdb=" CA TYR A 79 " pdb=" C TYR A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 5221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.449: 1276 3.449 - 6.898: 0 6.898 - 10.347: 0 10.347 - 13.796: 0 13.796 - 17.245: 1 Chirality restraints: 1277 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 -6.48 17.24 2.00e-01 2.50e+01 7.43e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CG LEU A 35 " pdb=" CB LEU A 35 " pdb=" CD1 LEU A 35 " pdb=" CD2 LEU A 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1274 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 502 " 0.019 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" C2C HEC C 502 " -0.191 2.00e-02 2.50e+03 pdb=" C3C HEC C 502 " 0.056 2.00e-02 2.50e+03 pdb=" C4C HEC C 502 " 0.009 2.00e-02 2.50e+03 pdb=" CAC HEC C 502 " 0.020 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " 0.029 2.00e-02 2.50e+03 pdb=" CHD HEC C 502 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC C 502 " 0.059 2.00e-02 2.50e+03 pdb=" NC HEC C 502 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 66 " -0.115 5.00e-02 4.00e+02 1.58e-01 4.02e+01 pdb=" N PRO A 67 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 147 " -0.111 5.00e-02 4.00e+02 1.55e-01 3.83e+01 pdb=" N PRO C 148 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO C 148 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO C 148 " -0.077 5.00e-02 4.00e+02 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 2 1.97 - 2.70: 387 2.70 - 3.44: 13234 3.44 - 4.17: 22624 4.17 - 4.90: 39169 Nonbonded interactions: 75416 Sorted by model distance: nonbonded pdb=" OD2 ASP C 375 " pdb=" O1D HEC C 502 " model vdw 1.241 3.040 nonbonded pdb=" CG ASP C 375 " pdb=" O1D HEC C 502 " model vdw 1.377 3.270 nonbonded pdb=" NE2 GLN A 46 " pdb=" OD1 ASN A 50 " model vdw 1.988 2.520 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.092 2.440 nonbonded pdb=" OG1 THR C 234 " pdb=" O PRO C 294 " model vdw 2.106 2.440 ... (remaining 75411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.070 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: 4.820 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.630 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 1.606 8835 Z= 2.184 Angle : 1.663 73.755 12078 Z= 0.722 Chirality : 0.485 17.245 1277 Planarity : 0.011 0.158 1568 Dihedral : 18.742 96.866 3212 Min Nonbonded Distance : 1.241 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.15 % Allowed : 32.66 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1083 helix: 0.00 (0.26), residues: 399 sheet: -1.14 (0.51), residues: 91 loop : -0.97 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 173 HIS 0.021 0.001 HIS C 422 PHE 0.018 0.002 PHE B 54 TYR 0.040 0.003 TYR A 182 ARG 0.021 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 304 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.4887 (tpt) cc_final: 0.4682 (tpp) REVERT: A 330 SER cc_start: 0.8253 (m) cc_final: 0.7989 (t) REVERT: A 438 TYR cc_start: 0.4133 (t80) cc_final: 0.3841 (t80) REVERT: A 439 ASP cc_start: 0.7416 (m-30) cc_final: 0.7004 (t0) REVERT: A 453 GLN cc_start: 0.8496 (tp40) cc_final: 0.8005 (mm-40) REVERT: A 514 MET cc_start: 0.6719 (mmp) cc_final: 0.6294 (mpp) REVERT: B 51 ILE cc_start: 0.8267 (mt) cc_final: 0.7989 (tp) REVERT: B 53 ASP cc_start: 0.8567 (m-30) cc_final: 0.8262 (t0) REVERT: B 93 LEU cc_start: 0.8556 (mt) cc_final: 0.8343 (tp) REVERT: B 96 HIS cc_start: 0.8304 (m-70) cc_final: 0.8051 (m90) REVERT: B 100 ASN cc_start: 0.8856 (m-40) cc_final: 0.8420 (m-40) REVERT: B 134 GLU cc_start: 0.7744 (mp0) cc_final: 0.7431 (mt-10) REVERT: C 107 ILE cc_start: 0.8649 (mp) cc_final: 0.8354 (mm) REVERT: C 284 SER cc_start: 0.8052 (t) cc_final: 0.7712 (p) outliers start: 19 outliers final: 10 residues processed: 316 average time/residue: 0.2325 time to fit residues: 96.4972 Evaluate side-chains 182 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.0570 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 58 ASN A 312 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 539 ASN C 326 ASN C 374 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 8835 Z= 0.298 Angle : 1.316 80.319 12078 Z= 0.505 Chirality : 0.045 0.199 1277 Planarity : 0.006 0.076 1568 Dihedral : 9.884 76.709 1299 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.76 % Allowed : 24.41 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: -0.37 (0.25), residues: 1083 helix: 0.67 (0.27), residues: 390 sheet: -0.92 (0.52), residues: 92 loop : -0.71 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 188 HIS 0.005 0.001 HIS C 260 PHE 0.017 0.002 PHE C 250 TYR 0.016 0.002 TYR C 135 ARG 0.005 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 199 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.8713 (ttp) cc_final: 0.8233 (ptm) REVERT: A 175 MET cc_start: 0.8043 (mtt) cc_final: 0.7775 (mtt) REVERT: A 211 ASP cc_start: 0.7951 (t0) cc_final: 0.7617 (t0) REVERT: A 312 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6597 (m-40) REVERT: A 322 MET cc_start: 0.4654 (mmt) cc_final: 0.4408 (mmt) REVERT: A 438 TYR cc_start: 0.4664 (t80) cc_final: 0.4046 (t80) REVERT: A 439 ASP cc_start: 0.7692 (m-30) cc_final: 0.6796 (t0) REVERT: A 483 THR cc_start: 0.5603 (m) cc_final: 0.4927 (p) REVERT: A 485 MET cc_start: 0.7385 (mpt) cc_final: 0.6878 (mpt) REVERT: B 53 ASP cc_start: 0.8543 (m-30) cc_final: 0.8113 (t0) REVERT: B 86 PHE cc_start: 0.7487 (t80) cc_final: 0.6679 (t80) REVERT: B 89 GLN cc_start: 0.8600 (mt0) cc_final: 0.7992 (mp10) REVERT: B 91 LYS cc_start: 0.9168 (mmmt) cc_final: 0.8726 (mmtp) REVERT: B 96 HIS cc_start: 0.8702 (m-70) cc_final: 0.8496 (m170) REVERT: B 100 ASN cc_start: 0.8792 (m-40) cc_final: 0.8445 (m-40) REVERT: B 140 LYS cc_start: 0.8534 (mtpt) cc_final: 0.7981 (mtpt) REVERT: C 107 ILE cc_start: 0.8631 (mp) cc_final: 0.8426 (mm) REVERT: C 123 TYR cc_start: 0.8152 (m-10) cc_final: 0.7919 (m-80) REVERT: C 210 PHE cc_start: 0.8527 (t80) cc_final: 0.8090 (t80) REVERT: C 284 SER cc_start: 0.8121 (t) cc_final: 0.7799 (p) outliers start: 51 outliers final: 25 residues processed: 234 average time/residue: 0.1968 time to fit residues: 64.1143 Evaluate side-chains 189 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 46 GLN A 203 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN C 374 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 8835 Z= 0.337 Angle : 1.254 71.368 12078 Z= 0.478 Chirality : 0.056 1.179 1277 Planarity : 0.006 0.063 1568 Dihedral : 9.712 77.674 1297 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.21 % Allowed : 22.49 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1083 helix: 1.12 (0.28), residues: 370 sheet: -0.31 (0.53), residues: 83 loop : -0.80 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 173 HIS 0.004 0.001 HIS B 64 PHE 0.022 0.002 PHE C 156 TYR 0.025 0.002 TYR B 142 ARG 0.017 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 184 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9049 (m) cc_final: 0.8731 (m) REVERT: A 211 ASP cc_start: 0.8174 (t0) cc_final: 0.7725 (t0) REVERT: A 375 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8745 (m) REVERT: A 483 THR cc_start: 0.6569 (m) cc_final: 0.5713 (p) REVERT: B 53 ASP cc_start: 0.8637 (m-30) cc_final: 0.8178 (t0) REVERT: B 56 GLN cc_start: 0.8678 (tt0) cc_final: 0.8387 (tt0) REVERT: B 96 HIS cc_start: 0.8903 (m-70) cc_final: 0.8582 (m170) REVERT: B 100 ASN cc_start: 0.8755 (m-40) cc_final: 0.8528 (m-40) REVERT: B 102 TYR cc_start: 0.7778 (m-80) cc_final: 0.7566 (m-10) REVERT: B 115 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7973 (p0) REVERT: C 107 ILE cc_start: 0.8736 (mp) cc_final: 0.8522 (mm) REVERT: C 118 MET cc_start: 0.8428 (tpt) cc_final: 0.8205 (tpt) REVERT: C 159 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8274 (t) REVERT: C 210 PHE cc_start: 0.8673 (t80) cc_final: 0.8216 (t80) REVERT: C 267 MET cc_start: 0.8843 (tpt) cc_final: 0.8523 (tpt) REVERT: C 284 SER cc_start: 0.8374 (t) cc_final: 0.8034 (p) outliers start: 55 outliers final: 30 residues processed: 223 average time/residue: 0.1912 time to fit residues: 60.9256 Evaluate side-chains 197 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.0570 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 8835 Z= 0.266 Angle : 1.065 81.735 12078 Z= 0.419 Chirality : 0.063 1.593 1277 Planarity : 0.005 0.071 1568 Dihedral : 9.331 76.241 1296 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.07 % Allowed : 23.95 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: -0.02 (0.26), residues: 1083 helix: 1.22 (0.28), residues: 368 sheet: -0.40 (0.52), residues: 92 loop : -0.70 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 173 HIS 0.003 0.001 HIS C 260 PHE 0.017 0.002 PHE C 158 TYR 0.016 0.001 TYR B 162 ARG 0.009 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 0.992 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 45 SER cc_start: 0.9078 (m) cc_final: 0.8774 (m) REVERT: A 211 ASP cc_start: 0.8236 (t0) cc_final: 0.7801 (t0) REVERT: A 375 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8765 (m) REVERT: A 438 TYR cc_start: 0.4939 (t80) cc_final: 0.4193 (t80) REVERT: A 453 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8115 (tp40) REVERT: A 483 THR cc_start: 0.6698 (m) cc_final: 0.5899 (p) REVERT: B 53 ASP cc_start: 0.8559 (m-30) cc_final: 0.8234 (t0) REVERT: B 96 HIS cc_start: 0.8956 (m-70) cc_final: 0.8612 (m90) REVERT: B 100 ASN cc_start: 0.8736 (m-40) cc_final: 0.8386 (m-40) REVERT: B 102 TYR cc_start: 0.7920 (m-80) cc_final: 0.7362 (m-10) REVERT: B 112 MET cc_start: 0.8377 (mtp) cc_final: 0.8090 (mtp) REVERT: C 107 ILE cc_start: 0.8847 (mp) cc_final: 0.8630 (mm) REVERT: C 210 PHE cc_start: 0.8703 (t80) cc_final: 0.8234 (t80) outliers start: 36 outliers final: 23 residues processed: 191 average time/residue: 0.1689 time to fit residues: 47.0963 Evaluate side-chains 175 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 98 GLN A 203 GLN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.7498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 8835 Z= 0.335 Angle : 1.118 83.994 12078 Z= 0.447 Chirality : 0.060 1.367 1277 Planarity : 0.006 0.068 1568 Dihedral : 9.518 81.661 1294 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 5.65 % Allowed : 22.94 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.10 (0.26), residues: 1083 helix: 1.14 (0.28), residues: 378 sheet: -0.07 (0.59), residues: 79 loop : -0.57 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 173 HIS 0.010 0.001 HIS A 110 PHE 0.029 0.002 PHE C 156 TYR 0.024 0.002 TYR B 162 ARG 0.008 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 176 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7416 (p0) cc_final: 0.6913 (p0) REVERT: A 45 SER cc_start: 0.9247 (m) cc_final: 0.9047 (m) REVERT: A 78 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7878 (t0) REVERT: A 137 MET cc_start: 0.7602 (ptt) cc_final: 0.7387 (ptt) REVERT: A 211 ASP cc_start: 0.8410 (t0) cc_final: 0.7994 (t0) REVERT: A 268 ILE cc_start: 0.7403 (pp) cc_final: 0.7078 (pp) REVERT: A 322 MET cc_start: 0.5267 (mmt) cc_final: 0.5043 (mmt) REVERT: A 330 SER cc_start: 0.8592 (t) cc_final: 0.8267 (m) REVERT: A 356 ASP cc_start: 0.8296 (m-30) cc_final: 0.8033 (m-30) REVERT: A 375 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8689 (m) REVERT: A 479 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7510 (mt) REVERT: B 53 ASP cc_start: 0.8694 (m-30) cc_final: 0.8329 (t0) REVERT: B 89 GLN cc_start: 0.9104 (mt0) cc_final: 0.8205 (mt0) REVERT: B 136 GLU cc_start: 0.7896 (pm20) cc_final: 0.7336 (pm20) REVERT: C 107 ILE cc_start: 0.9021 (mp) cc_final: 0.8798 (mm) REVERT: C 210 PHE cc_start: 0.8895 (t80) cc_final: 0.8451 (t80) REVERT: C 395 MET cc_start: 0.8811 (ttp) cc_final: 0.8452 (ttt) outliers start: 50 outliers final: 27 residues processed: 214 average time/residue: 0.1729 time to fit residues: 53.4637 Evaluate side-chains 179 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN B 56 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8835 Z= 0.257 Angle : 1.065 83.166 12078 Z= 0.418 Chirality : 0.061 1.478 1277 Planarity : 0.005 0.064 1568 Dihedral : 9.382 80.305 1292 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.07 % Allowed : 24.86 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.17 (0.26), residues: 1083 helix: 1.20 (0.28), residues: 376 sheet: -0.10 (0.58), residues: 82 loop : -0.51 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 173 HIS 0.005 0.001 HIS A 110 PHE 0.016 0.001 PHE A 270 TYR 0.031 0.002 TYR A 79 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7491 (p0) cc_final: 0.6994 (p0) REVERT: A 45 SER cc_start: 0.9236 (m) cc_final: 0.9034 (m) REVERT: A 54 MET cc_start: 0.9004 (ttp) cc_final: 0.8791 (ttp) REVERT: A 151 CYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8494 (m) REVERT: A 211 ASP cc_start: 0.8413 (t0) cc_final: 0.8012 (t0) REVERT: A 356 ASP cc_start: 0.8352 (m-30) cc_final: 0.8051 (m-30) REVERT: A 375 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8552 (m) REVERT: A 453 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8274 (tp-100) REVERT: B 89 GLN cc_start: 0.9044 (mt0) cc_final: 0.8225 (mt0) REVERT: B 102 TYR cc_start: 0.8074 (m-80) cc_final: 0.7792 (m-80) REVERT: B 136 GLU cc_start: 0.7931 (pm20) cc_final: 0.7383 (pm20) REVERT: C 107 ILE cc_start: 0.9031 (mp) cc_final: 0.8814 (mm) REVERT: C 118 MET cc_start: 0.8714 (tpt) cc_final: 0.8191 (tpt) REVERT: C 210 PHE cc_start: 0.8889 (t80) cc_final: 0.8507 (t80) REVERT: C 395 MET cc_start: 0.8664 (ttp) cc_final: 0.8409 (ttt) REVERT: C 410 GLU cc_start: 0.8905 (tp30) cc_final: 0.8643 (tp30) outliers start: 36 outliers final: 29 residues processed: 181 average time/residue: 0.1790 time to fit residues: 46.3225 Evaluate side-chains 165 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 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 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8835 Z= 0.258 Angle : 1.062 83.063 12078 Z= 0.413 Chirality : 0.060 1.481 1277 Planarity : 0.005 0.058 1568 Dihedral : 9.217 80.136 1291 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.86 % Allowed : 24.41 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.21 (0.26), residues: 1083 helix: 1.22 (0.28), residues: 382 sheet: -0.18 (0.58), residues: 81 loop : -0.47 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 173 HIS 0.008 0.001 HIS A 110 PHE 0.014 0.001 PHE A 270 TYR 0.031 0.002 TYR A 271 ARG 0.005 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7602 (p0) cc_final: 0.7109 (p0) REVERT: A 61 GLN cc_start: 0.7668 (mp10) cc_final: 0.7386 (mm-40) REVERT: A 151 CYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8539 (m) REVERT: A 211 ASP cc_start: 0.8436 (t0) cc_final: 0.8074 (t0) REVERT: A 356 ASP cc_start: 0.8438 (m-30) cc_final: 0.8141 (m-30) REVERT: A 375 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8497 (m) REVERT: A 453 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8276 (tp-100) REVERT: B 89 GLN cc_start: 0.9119 (mt0) cc_final: 0.8289 (mt0) REVERT: B 91 LYS cc_start: 0.9356 (mmmt) cc_final: 0.9071 (mmmm) REVERT: B 136 GLU cc_start: 0.7910 (pm20) cc_final: 0.7330 (pm20) REVERT: C 107 ILE cc_start: 0.9062 (mp) cc_final: 0.8842 (mm) REVERT: C 108 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7292 (mtm110) REVERT: C 118 MET cc_start: 0.8676 (tpt) cc_final: 0.8085 (tpt) REVERT: C 395 MET cc_start: 0.8661 (ttp) cc_final: 0.8422 (ttt) REVERT: C 410 GLU cc_start: 0.8917 (tp30) cc_final: 0.8607 (tp30) outliers start: 43 outliers final: 28 residues processed: 187 average time/residue: 0.1893 time to fit residues: 49.8732 Evaluate side-chains 165 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 chunk 31 optimal weight: 0.2980 chunk 20 optimal weight: 0.0170 chunk 66 optimal weight: 0.0010 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 overall best weight: 0.1430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.8020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 8835 Z= 0.211 Angle : 1.072 83.199 12078 Z= 0.417 Chirality : 0.060 1.489 1277 Planarity : 0.005 0.063 1568 Dihedral : 9.039 79.488 1291 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.73 % Allowed : 25.76 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.20 (0.26), residues: 1083 helix: 1.32 (0.28), residues: 375 sheet: -0.22 (0.57), residues: 81 loop : -0.53 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 173 HIS 0.003 0.001 HIS C 260 PHE 0.014 0.001 PHE C 156 TYR 0.047 0.002 TYR A 255 ARG 0.003 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8091 (m-30) cc_final: 0.7794 (t0) REVERT: A 37 ASP cc_start: 0.7460 (p0) cc_final: 0.6921 (p0) REVERT: A 54 MET cc_start: 0.8981 (ttp) cc_final: 0.8707 (ttp) REVERT: A 151 CYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8587 (m) REVERT: A 193 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8608 (mmtm) REVERT: A 211 ASP cc_start: 0.8316 (t0) cc_final: 0.7821 (t0) REVERT: A 220 ASN cc_start: 0.8661 (t0) cc_final: 0.8421 (t0) REVERT: A 271 TYR cc_start: 0.7547 (m-80) cc_final: 0.7172 (m-80) REVERT: A 356 ASP cc_start: 0.8449 (m-30) cc_final: 0.8007 (m-30) REVERT: A 360 GLU cc_start: 0.8420 (pm20) cc_final: 0.8197 (mp0) REVERT: A 453 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8290 (tp-100) REVERT: B 89 GLN cc_start: 0.9142 (mt0) cc_final: 0.8329 (mt0) REVERT: B 91 LYS cc_start: 0.9361 (mmmt) cc_final: 0.9078 (mmmm) REVERT: B 136 GLU cc_start: 0.7949 (pm20) cc_final: 0.7384 (pm20) REVERT: C 107 ILE cc_start: 0.9043 (mp) cc_final: 0.8831 (mm) REVERT: C 108 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7195 (mtm110) REVERT: C 118 MET cc_start: 0.8506 (tpt) cc_final: 0.8020 (tpt) outliers start: 33 outliers final: 23 residues processed: 184 average time/residue: 0.1868 time to fit residues: 48.3947 Evaluate side-chains 171 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.1980 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.0050 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.8165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 8835 Z= 0.230 Angle : 1.076 83.267 12078 Z= 0.420 Chirality : 0.060 1.482 1277 Planarity : 0.005 0.054 1568 Dihedral : 9.014 80.341 1291 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.28 % Allowed : 26.78 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.21 (0.26), residues: 1083 helix: 1.41 (0.29), residues: 375 sheet: -0.01 (0.63), residues: 59 loop : -0.61 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 173 HIS 0.004 0.001 HIS A 110 PHE 0.015 0.001 PHE A 270 TYR 0.042 0.002 TYR A 255 ARG 0.005 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7522 (p0) cc_final: 0.6987 (p0) REVERT: A 54 MET cc_start: 0.9014 (ttp) cc_final: 0.8764 (ttp) REVERT: A 151 CYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8581 (m) REVERT: A 193 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8566 (mmtm) REVERT: A 211 ASP cc_start: 0.8356 (t0) cc_final: 0.7928 (t0) REVERT: A 220 ASN cc_start: 0.8760 (t0) cc_final: 0.8478 (t0) REVERT: A 356 ASP cc_start: 0.8469 (m-30) cc_final: 0.8012 (m-30) REVERT: A 360 GLU cc_start: 0.8429 (pm20) cc_final: 0.8208 (mp0) REVERT: A 453 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8312 (tp-100) REVERT: B 89 GLN cc_start: 0.9243 (mt0) cc_final: 0.8353 (mp10) REVERT: B 106 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: B 136 GLU cc_start: 0.7993 (pm20) cc_final: 0.7520 (pm20) REVERT: C 107 ILE cc_start: 0.9055 (mp) cc_final: 0.8841 (mm) REVERT: C 108 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7180 (mtm110) REVERT: C 118 MET cc_start: 0.8558 (tpt) cc_final: 0.8000 (tpt) REVERT: C 395 MET cc_start: 0.8262 (ttp) cc_final: 0.8030 (ttp) outliers start: 29 outliers final: 21 residues processed: 175 average time/residue: 0.1875 time to fit residues: 46.4899 Evaluate side-chains 165 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.8607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 8835 Z= 0.316 Angle : 1.100 82.986 12078 Z= 0.435 Chirality : 0.062 1.481 1277 Planarity : 0.005 0.066 1568 Dihedral : 9.360 81.085 1291 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 2.82 % Allowed : 27.12 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.22 (0.26), residues: 1083 helix: 1.35 (0.28), residues: 376 sheet: 0.06 (0.64), residues: 61 loop : -0.56 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 173 HIS 0.010 0.001 HIS A 110 PHE 0.012 0.002 PHE A 270 TYR 0.045 0.002 TYR A 255 ARG 0.006 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7764 (p0) cc_final: 0.7161 (p0) REVERT: A 151 CYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8573 (m) REVERT: A 193 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8586 (mmtm) REVERT: A 211 ASP cc_start: 0.8424 (t0) cc_final: 0.8039 (t0) REVERT: A 271 TYR cc_start: 0.7754 (m-80) cc_final: 0.7361 (m-80) REVERT: A 356 ASP cc_start: 0.8533 (m-30) cc_final: 0.8130 (m-30) REVERT: A 453 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8390 (tp-100) REVERT: B 89 GLN cc_start: 0.9291 (mt0) cc_final: 0.9061 (mt0) REVERT: B 136 GLU cc_start: 0.8039 (pm20) cc_final: 0.7507 (pm20) REVERT: C 107 ILE cc_start: 0.9079 (mp) cc_final: 0.8864 (mm) REVERT: C 108 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7393 (mtm110) REVERT: C 267 MET cc_start: 0.9142 (tpt) cc_final: 0.8340 (tpt) outliers start: 25 outliers final: 21 residues processed: 155 average time/residue: 0.2016 time to fit residues: 43.6534 Evaluate side-chains 153 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078150 restraints weight = 17167.288| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.08 r_work: 0.2955 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.8711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 8835 Z= 0.239 Angle : 1.072 82.746 12078 Z= 0.420 Chirality : 0.061 1.497 1277 Planarity : 0.005 0.056 1568 Dihedral : 9.156 81.470 1289 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 3.16 % Allowed : 26.55 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.23 (0.26), residues: 1083 helix: 1.36 (0.28), residues: 375 sheet: 0.02 (0.65), residues: 62 loop : -0.55 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 173 HIS 0.005 0.001 HIS A 110 PHE 0.014 0.001 PHE A 270 TYR 0.039 0.002 TYR A 255 ARG 0.003 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.62 seconds wall clock time: 40 minutes 30.53 seconds (2430.53 seconds total)