Starting phenix.real_space_refine on Mon Apr 28 05:47:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chx_45604/04_2025/9chx_45604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chx_45604/04_2025/9chx_45604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chx_45604/04_2025/9chx_45604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chx_45604/04_2025/9chx_45604.map" model { file = "/net/cci-nas-00/data/ceres_data/9chx_45604/04_2025/9chx_45604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chx_45604/04_2025/9chx_45604.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4644 2.51 5 N 1164 2.21 5 O 1273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7129 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3450 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 422} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2792 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 20, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'CAU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.26, per 1000 atoms: 0.74 Number of scatterers: 7129 At special positions: 0 Unit cell: (68.85, 84.15, 155.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1273 8.00 N 1164 7.00 C 4644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 971.2 milliseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 54.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 32 through 60 removed outlier: 3.581A pdb=" N ILE A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 97 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 103 through 137 removed outlier: 3.907A pdb=" N GLU A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 146 through 171 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 209 through 226 Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.801A pdb=" N ALA A 232 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.882A pdb=" N ILE A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.928A pdb=" N LYS A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.791A pdb=" N LEU A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 394 through 421 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 429 through 444 removed outlier: 4.127A pdb=" N ASN A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.520A pdb=" N ILE A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 removed outlier: 3.800A pdb=" N ILE A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 73 removed outlier: 4.028A pdb=" N GLN B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 105 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.577A pdb=" N THR B 156 " --> pdb=" O CYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.695A pdb=" N TYR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.709A pdb=" N LEU B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.779A pdb=" N MET B 346 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 Processing helix chain 'B' and resid 353 through 369 removed outlier: 3.514A pdb=" N GLU B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 64 removed outlier: 3.965A pdb=" N ALA C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.502A pdb=" N ILE B 80 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 276 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE B 304 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 278 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 143 through 145 Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.984A pdb=" N VAL C 4 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR C 75 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR C 6 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS C 73 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 98 " --> pdb=" O MET C 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.237A pdb=" N HIS C 25 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU C 103 " --> pdb=" O HIS C 25 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2232 1.34 - 1.46: 1723 1.46 - 1.58: 3277 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 7305 Sorted by residual: bond pdb=" C9 FK5 C 201 " pdb=" O4 FK5 C 201 " ideal model delta sigma weight residual 1.206 1.409 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C1 FK5 C 201 " pdb=" O2 FK5 C 201 " ideal model delta sigma weight residual 1.211 1.407 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C22 FK5 C 201 " pdb=" O9 FK5 C 201 " ideal model delta sigma weight residual 1.215 1.407 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" C8 FK5 C 201 " pdb=" O3 FK5 C 201 " ideal model delta sigma weight residual 1.232 1.410 -0.178 2.00e-02 2.50e+03 7.94e+01 bond pdb=" C8 FK5 C 201 " pdb=" C9 FK5 C 201 " ideal model delta sigma weight residual 1.537 1.396 0.141 2.00e-02 2.50e+03 4.95e+01 ... (remaining 7300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 9701 2.00 - 3.99: 169 3.99 - 5.99: 30 5.99 - 7.99: 8 7.99 - 9.98: 4 Bond angle restraints: 9912 Sorted by residual: angle pdb=" N GLN B 193 " pdb=" CA GLN B 193 " pdb=" C GLN B 193 " ideal model delta sigma weight residual 114.56 110.40 4.16 1.27e+00 6.20e-01 1.07e+01 angle pdb=" C2 FK5 C 201 " pdb=" C1 FK5 C 201 " pdb=" O1 FK5 C 201 " ideal model delta sigma weight residual 112.57 122.39 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C27 FK5 C 201 " pdb=" C28 FK5 C 201 " pdb=" C29 FK5 C 201 " ideal model delta sigma weight residual 127.93 119.24 8.69 3.00e+00 1.11e-01 8.39e+00 angle pdb=" CA LEU B 364 " pdb=" CB LEU B 364 " pdb=" CG LEU B 364 " ideal model delta sigma weight residual 116.30 106.32 9.98 3.50e+00 8.16e-02 8.14e+00 angle pdb=" C VAL A 206 " pdb=" CA VAL A 206 " pdb=" CB VAL A 206 " ideal model delta sigma weight residual 111.20 107.89 3.31 1.24e+00 6.50e-01 7.13e+00 ... (remaining 9907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 4283 35.74 - 71.49: 81 71.49 - 107.23: 9 107.23 - 142.97: 2 142.97 - 178.72: 6 Dihedral angle restraints: 4381 sinusoidal: 1795 harmonic: 2586 Sorted by residual: dihedral pdb=" C13 FK5 C 201 " pdb=" C14 FK5 C 201 " pdb=" C15 FK5 C 201 " pdb=" O8 FK5 C 201 " ideal model delta sinusoidal sigma weight residual 108.57 -72.71 -178.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 FK5 C 201 " pdb=" C14 FK5 C 201 " pdb=" C15 FK5 C 201 " pdb=" O8 FK5 C 201 " ideal model delta sinusoidal sigma weight residual -11.37 167.10 -178.47 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C13 FK5 C 201 " pdb=" C14 FK5 C 201 " pdb=" C15 FK5 C 201 " pdb=" C16 FK5 C 201 " ideal model delta sinusoidal sigma weight residual -123.85 48.96 -172.81 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 785 0.043 - 0.086: 268 0.086 - 0.129: 51 0.129 - 0.172: 9 0.172 - 0.215: 3 Chirality restraints: 1116 Sorted by residual: chirality pdb=" C10 FK5 C 201 " pdb=" C11 FK5 C 201 " pdb=" C9 FK5 C 201 " pdb=" O5 FK5 C 201 " both_signs ideal model delta sigma weight residual False 2.69 2.47 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C26 FK5 C 201 " pdb=" C25 FK5 C 201 " pdb=" C27 FK5 C 201 " pdb=" O1 FK5 C 201 " both_signs ideal model delta sigma weight residual False -2.61 -2.40 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C16 CAU A 501 " pdb=" C15 CAU A 501 " pdb=" C18 CAU A 501 " pdb=" O17 CAU A 501 " both_signs ideal model delta sigma weight residual False 2.31 2.49 -0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 1113 not shown) Planarity restraints: 1247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 FK5 C 201 " -0.126 2.00e-02 2.50e+03 1.35e-01 2.29e+02 pdb=" C27 FK5 C 201 " 0.052 2.00e-02 2.50e+03 pdb=" C28 FK5 C 201 " 0.208 2.00e-02 2.50e+03 pdb=" C29 FK5 C 201 " -0.169 2.00e-02 2.50e+03 pdb=" C42 FK5 C 201 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 FK5 C 201 " -0.075 2.00e-02 2.50e+03 8.33e-02 8.68e+01 pdb=" C19 FK5 C 201 " 0.023 2.00e-02 2.50e+03 pdb=" C20 FK5 C 201 " 0.133 2.00e-02 2.50e+03 pdb=" C21 FK5 C 201 " -0.103 2.00e-02 2.50e+03 pdb=" C37 FK5 C 201 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 77 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO C 78 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 78 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 78 " 0.026 5.00e-02 4.00e+02 ... (remaining 1244 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 145 2.70 - 3.25: 7080 3.25 - 3.80: 10807 3.80 - 4.35: 13634 4.35 - 4.90: 23055 Nonbonded interactions: 54721 Sorted by model distance: nonbonded pdb=" OG SER B 293 " pdb=" O PHE B 298 " model vdw 2.146 3.040 nonbonded pdb=" OG SER A 323 " pdb=" O THR B 13 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR C 6 " pdb=" OE1 GLN C 70 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR C 82 " pdb=" O3 FK5 C 201 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP A 231 " pdb=" NZ LYS A 236 " model vdw 2.313 3.120 ... (remaining 54716 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.203 7307 Z= 0.333 Angle : 0.698 9.985 9916 Z= 0.356 Chirality : 0.045 0.215 1116 Planarity : 0.006 0.135 1247 Dihedral : 17.123 178.718 2707 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.29), residues: 879 helix: 0.33 (0.25), residues: 444 sheet: -0.36 (0.60), residues: 74 loop : -1.13 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 109 HIS 0.011 0.001 HIS B 280 PHE 0.019 0.002 PHE A 223 TYR 0.012 0.001 TYR B 259 ARG 0.002 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.14086 ( 340) hydrogen bonds : angle 5.60741 ( 978) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.62589 ( 4) covalent geometry : bond 0.00686 ( 7305) covalent geometry : angle 0.69788 ( 9912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: C 100 ASP cc_start: 0.7046 (t70) cc_final: 0.6704 (t0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1567 time to fit residues: 24.0021 Evaluate side-chains 79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.0070 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 435 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN C 94 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.198581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.157599 restraints weight = 8208.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.158856 restraints weight = 7106.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161580 restraints weight = 6088.493| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7307 Z= 0.179 Angle : 0.625 11.616 9916 Z= 0.326 Chirality : 0.044 0.165 1116 Planarity : 0.005 0.078 1247 Dihedral : 15.580 174.637 1066 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.57 % Allowed : 11.14 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.29), residues: 879 helix: 0.39 (0.25), residues: 449 sheet: -1.09 (0.59), residues: 70 loop : -0.98 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 109 HIS 0.007 0.001 HIS B 280 PHE 0.020 0.002 PHE A 242 TYR 0.027 0.002 TYR B 174 ARG 0.003 0.000 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 340) hydrogen bonds : angle 4.63238 ( 978) SS BOND : bond 0.00477 ( 2) SS BOND : angle 0.93158 ( 4) covalent geometry : bond 0.00422 ( 7305) covalent geometry : angle 0.62456 ( 9912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: C 100 ASP cc_start: 0.7345 (t70) cc_final: 0.6875 (t0) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.1654 time to fit residues: 19.8812 Evaluate side-chains 84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 284 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN C 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.199719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.158242 restraints weight = 8294.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.160999 restraints weight = 6529.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.163020 restraints weight = 5302.969| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7307 Z= 0.128 Angle : 0.552 9.301 9916 Z= 0.288 Chirality : 0.041 0.133 1116 Planarity : 0.004 0.058 1247 Dihedral : 14.855 173.688 1066 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.97 % Allowed : 14.94 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.29), residues: 879 helix: 0.58 (0.25), residues: 448 sheet: -1.19 (0.58), residues: 70 loop : -0.89 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 109 HIS 0.004 0.001 HIS B 280 PHE 0.016 0.001 PHE A 242 TYR 0.016 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 340) hydrogen bonds : angle 4.35131 ( 978) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.61717 ( 4) covalent geometry : bond 0.00291 ( 7305) covalent geometry : angle 0.55210 ( 9912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.805 Fit side-chains REVERT: A 179 GLN cc_start: 0.8776 (pm20) cc_final: 0.8545 (tp-100) REVERT: B 322 LYS cc_start: 0.7872 (mttm) cc_final: 0.7575 (mttm) REVERT: C 100 ASP cc_start: 0.7316 (t70) cc_final: 0.6764 (t0) outliers start: 15 outliers final: 10 residues processed: 89 average time/residue: 0.1535 time to fit residues: 20.1490 Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 0.3980 chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.190346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.148799 restraints weight = 8390.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.150307 restraints weight = 6633.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.152484 restraints weight = 5893.341| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 7307 Z= 0.257 Angle : 0.773 17.986 9916 Z= 0.392 Chirality : 0.048 0.234 1116 Planarity : 0.005 0.062 1247 Dihedral : 14.936 173.539 1066 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.15 % Allowed : 17.43 % Favored : 79.42 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.86 (0.29), residues: 879 helix: 0.13 (0.25), residues: 446 sheet: -1.06 (0.55), residues: 80 loop : -1.26 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 109 HIS 0.006 0.001 HIS B 280 PHE 0.017 0.002 PHE A 258 TYR 0.017 0.002 TYR B 139 ARG 0.003 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 340) hydrogen bonds : angle 4.78957 ( 978) SS BOND : bond 0.01156 ( 2) SS BOND : angle 9.19522 ( 4) covalent geometry : bond 0.00629 ( 7305) covalent geometry : angle 0.75028 ( 9912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.777 Fit side-chains REVERT: B 73 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: C 100 ASP cc_start: 0.7379 (t70) cc_final: 0.6819 (t0) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.1472 time to fit residues: 20.4865 Evaluate side-chains 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 0.4980 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.197901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.157201 restraints weight = 8266.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.160034 restraints weight = 6542.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.162198 restraints weight = 5339.595| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7307 Z= 0.121 Angle : 0.590 11.158 9916 Z= 0.306 Chirality : 0.041 0.154 1116 Planarity : 0.004 0.051 1247 Dihedral : 14.320 173.202 1066 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.15 % Allowed : 19.13 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 879 helix: 0.60 (0.26), residues: 442 sheet: -0.95 (0.55), residues: 80 loop : -0.96 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 109 HIS 0.005 0.001 HIS C 94 PHE 0.016 0.001 PHE A 242 TYR 0.015 0.001 TYR B 139 ARG 0.002 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 340) hydrogen bonds : angle 4.34407 ( 978) SS BOND : bond 0.00487 ( 2) SS BOND : angle 6.69093 ( 4) covalent geometry : bond 0.00272 ( 7305) covalent geometry : angle 0.57433 ( 9912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.738 Fit side-chains REVERT: A 145 LEU cc_start: 0.4138 (OUTLIER) cc_final: 0.3931 (tt) REVERT: B 144 PHE cc_start: 0.7794 (m-80) cc_final: 0.7570 (m-80) REVERT: C 100 ASP cc_start: 0.7278 (t70) cc_final: 0.6658 (t0) outliers start: 24 outliers final: 16 residues processed: 96 average time/residue: 0.1431 time to fit residues: 20.1520 Evaluate side-chains 90 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 52 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 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 179 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.199415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.158755 restraints weight = 8287.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.160631 restraints weight = 6519.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.163398 restraints weight = 5359.559| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7307 Z= 0.125 Angle : 0.592 10.127 9916 Z= 0.304 Chirality : 0.042 0.169 1116 Planarity : 0.004 0.048 1247 Dihedral : 13.934 172.708 1066 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.28 % Allowed : 19.66 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 879 helix: 0.66 (0.26), residues: 445 sheet: -1.00 (0.55), residues: 80 loop : -0.90 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 99 HIS 0.005 0.001 HIS C 94 PHE 0.030 0.001 PHE A 104 TYR 0.015 0.001 TYR B 139 ARG 0.002 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 340) hydrogen bonds : angle 4.26405 ( 978) SS BOND : bond 0.00391 ( 2) SS BOND : angle 6.15641 ( 4) covalent geometry : bond 0.00284 ( 7305) covalent geometry : angle 0.57900 ( 9912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.722 Fit side-chains REVERT: A 107 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: A 145 LEU cc_start: 0.4236 (OUTLIER) cc_final: 0.3998 (tt) REVERT: A 362 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6364 (mtp85) REVERT: B 73 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: B 98 MET cc_start: 0.5873 (mmt) cc_final: 0.4983 (mmt) REVERT: C 100 ASP cc_start: 0.7344 (t70) cc_final: 0.6764 (t0) outliers start: 25 outliers final: 16 residues processed: 95 average time/residue: 0.1532 time to fit residues: 20.8259 Evaluate side-chains 97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.199778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.161240 restraints weight = 8585.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.162203 restraints weight = 8558.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165135 restraints weight = 6847.045| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7307 Z= 0.124 Angle : 0.582 8.504 9916 Z= 0.300 Chirality : 0.041 0.153 1116 Planarity : 0.004 0.048 1247 Dihedral : 13.577 172.288 1066 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.54 % Allowed : 19.66 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 879 helix: 0.70 (0.26), residues: 446 sheet: -0.98 (0.56), residues: 80 loop : -0.84 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 99 HIS 0.005 0.001 HIS C 94 PHE 0.026 0.001 PHE A 104 TYR 0.014 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 340) hydrogen bonds : angle 4.21970 ( 978) SS BOND : bond 0.00271 ( 2) SS BOND : angle 5.43981 ( 4) covalent geometry : bond 0.00283 ( 7305) covalent geometry : angle 0.57172 ( 9912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.714 Fit side-chains REVERT: A 107 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: A 145 LEU cc_start: 0.4628 (OUTLIER) cc_final: 0.4380 (tt) REVERT: A 362 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6571 (mtp85) REVERT: B 73 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: B 276 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7748 (mm) REVERT: C 100 ASP cc_start: 0.7371 (t70) cc_final: 0.6857 (t0) outliers start: 27 outliers final: 18 residues processed: 98 average time/residue: 0.1714 time to fit residues: 23.9923 Evaluate side-chains 98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 289 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 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 = 0.4569 r_free = 0.4569 target = 0.204510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.169106 restraints weight = 8685.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.171793 restraints weight = 9195.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.173961 restraints weight = 7498.926| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7307 Z= 0.107 Angle : 0.554 10.159 9916 Z= 0.284 Chirality : 0.040 0.224 1116 Planarity : 0.004 0.048 1247 Dihedral : 13.279 171.688 1066 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.62 % Allowed : 21.49 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.08 (0.30), residues: 879 helix: 0.78 (0.26), residues: 451 sheet: -1.03 (0.54), residues: 83 loop : -0.83 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 99 HIS 0.003 0.001 HIS B 280 PHE 0.025 0.001 PHE A 104 TYR 0.014 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 340) hydrogen bonds : angle 4.09467 ( 978) SS BOND : bond 0.01298 ( 2) SS BOND : angle 3.09996 ( 4) covalent geometry : bond 0.00230 ( 7305) covalent geometry : angle 0.55086 ( 9912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.795 Fit side-chains REVERT: A 145 LEU cc_start: 0.4692 (OUTLIER) cc_final: 0.4440 (tt) REVERT: A 362 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6538 (mtp85) REVERT: B 73 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: B 137 ILE cc_start: 0.5359 (mt) cc_final: 0.5151 (mt) REVERT: B 276 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7769 (mm) REVERT: C 100 ASP cc_start: 0.7299 (t70) cc_final: 0.6815 (t0) outliers start: 20 outliers final: 11 residues processed: 95 average time/residue: 0.1736 time to fit residues: 23.7194 Evaluate side-chains 92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.0270 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 338 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.200304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.163491 restraints weight = 8766.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166109 restraints weight = 9655.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.167927 restraints weight = 7133.509| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7307 Z= 0.141 Angle : 0.604 9.024 9916 Z= 0.308 Chirality : 0.042 0.185 1116 Planarity : 0.004 0.047 1247 Dihedral : 13.490 174.390 1066 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.15 % Allowed : 22.28 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.09 (0.30), residues: 879 helix: 0.80 (0.26), residues: 442 sheet: -1.04 (0.56), residues: 80 loop : -0.83 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 99 HIS 0.004 0.001 HIS B 280 PHE 0.021 0.001 PHE A 104 TYR 0.015 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 340) hydrogen bonds : angle 4.21192 ( 978) SS BOND : bond 0.00908 ( 2) SS BOND : angle 2.75980 ( 4) covalent geometry : bond 0.00330 ( 7305) covalent geometry : angle 0.60129 ( 9912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.776 Fit side-chains REVERT: A 145 LEU cc_start: 0.4694 (OUTLIER) cc_final: 0.4455 (tt) REVERT: A 362 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6586 (mtp85) REVERT: B 73 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: B 276 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7821 (mm) REVERT: C 100 ASP cc_start: 0.7399 (t70) cc_final: 0.6887 (t0) outliers start: 24 outliers final: 16 residues processed: 97 average time/residue: 0.1583 time to fit residues: 22.0801 Evaluate side-chains 98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 289 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 2 optimal weight: 0.0170 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 49 optimal weight: 0.0670 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.205185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.168900 restraints weight = 8707.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.170423 restraints weight = 9193.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.172996 restraints weight = 7524.100| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7307 Z= 0.102 Angle : 0.546 8.492 9916 Z= 0.278 Chirality : 0.040 0.161 1116 Planarity : 0.004 0.049 1247 Dihedral : 13.240 172.447 1066 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.49 % Allowed : 22.80 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.05 (0.30), residues: 879 helix: 0.89 (0.26), residues: 448 sheet: -1.03 (0.54), residues: 83 loop : -0.73 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 109 HIS 0.003 0.001 HIS B 280 PHE 0.023 0.001 PHE A 104 TYR 0.015 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 340) hydrogen bonds : angle 4.03946 ( 978) SS BOND : bond 0.00779 ( 2) SS BOND : angle 2.16862 ( 4) covalent geometry : bond 0.00220 ( 7305) covalent geometry : angle 0.54454 ( 9912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.830 Fit side-chains REVERT: A 145 LEU cc_start: 0.4554 (OUTLIER) cc_final: 0.4342 (tt) REVERT: B 73 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: B 137 ILE cc_start: 0.5291 (mt) cc_final: 0.5080 (mt) REVERT: B 276 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7741 (mm) REVERT: C 100 ASP cc_start: 0.7308 (t70) cc_final: 0.6794 (t0) outliers start: 19 outliers final: 12 residues processed: 96 average time/residue: 0.1498 time to fit residues: 21.1687 Evaluate side-chains 93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 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 = 0.4576 r_free = 0.4576 target = 0.204578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.169924 restraints weight = 8576.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.170471 restraints weight = 9035.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.172918 restraints weight = 7503.900| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7307 Z= 0.107 Angle : 0.556 8.448 9916 Z= 0.283 Chirality : 0.041 0.154 1116 Planarity : 0.003 0.048 1247 Dihedral : 13.244 172.885 1066 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.62 % Allowed : 22.67 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.12 (0.30), residues: 879 helix: 0.94 (0.26), residues: 448 sheet: -0.90 (0.56), residues: 78 loop : -0.72 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 109 HIS 0.003 0.001 HIS B 280 PHE 0.021 0.001 PHE A 104 TYR 0.014 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 340) hydrogen bonds : angle 4.03520 ( 978) SS BOND : bond 0.00805 ( 2) SS BOND : angle 2.13512 ( 4) covalent geometry : bond 0.00236 ( 7305) covalent geometry : angle 0.55420 ( 9912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2295.04 seconds wall clock time: 40 minutes 34.60 seconds (2434.60 seconds total)