Starting phenix.real_space_refine on Wed Sep 17 08:16:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chx_45604/09_2025/9chx_45604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chx_45604/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9chx_45604/09_2025/9chx_45604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chx_45604/09_2025/9chx_45604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9chx_45604/09_2025/9chx_45604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chx_45604/09_2025/9chx_45604.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} 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: {'ARG:plan': 2, 'GLU: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: 1.88, per 1000 atoms: 0.26 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: 0.62 Conformation dependent library (CDL) restraints added in 388.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 0.95 Time building geometry restraints manager: 0.82 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: 2.270 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 272 TYR 0.012 0.001 TYR B 259 PHE 0.019 0.002 PHE A 223 TRP 0.016 0.002 TRP A 109 HIS 0.011 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00686 ( 7305) covalent geometry : angle 0.69788 ( 9912) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.62589 ( 4) hydrogen bonds : bond 0.14086 ( 340) hydrogen bonds : angle 5.60741 ( 978) *********************** 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 : 0.302 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: 0.0705 time to fit residues: 10.9093 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 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 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4485 r_free = 0.4485 target = 0.202967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.161992 restraints weight = 8313.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.164013 restraints weight = 6891.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.166220 restraints weight = 6086.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.167712 restraints weight = 3917.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168386 restraints weight = 3664.282| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1072 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= 0.137 Angle : 0.573 9.969 9916 Z= 0.300 Chirality : 0.042 0.138 1116 Planarity : 0.004 0.073 1247 Dihedral : 15.716 175.339 1066 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.31 % Allowed : 10.75 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.29), residues: 879 helix: 0.58 (0.26), residues: 449 sheet: -1.05 (0.59), residues: 70 loop : -0.94 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.027 0.002 TYR B 174 PHE 0.019 0.001 PHE A 242 TRP 0.014 0.001 TRP A 109 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7305) covalent geometry : angle 0.57253 ( 9912) SS BOND : bond 0.00299 ( 2) SS BOND : angle 1.64332 ( 4) hydrogen bonds : bond 0.04423 ( 340) hydrogen bonds : angle 4.49159 ( 978) *********************** 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 91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.318 Fit side-chains REVERT: B 174 TYR cc_start: 0.7405 (t80) cc_final: 0.7189 (t80) REVERT: C 100 ASP cc_start: 0.7298 (t70) cc_final: 0.6822 (t0) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.0674 time to fit residues: 8.5770 Evaluate side-chains 86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 333 MET Chi-restraints excluded: chain B residue 50 MET 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 60 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.200813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.160152 restraints weight = 8253.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162967 restraints weight = 6557.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.165126 restraints weight = 5386.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165600 restraints weight = 3653.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.166202 restraints weight = 3698.866| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.1296 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= 0.126 Angle : 0.551 9.010 9916 Z= 0.286 Chirality : 0.041 0.133 1116 Planarity : 0.004 0.057 1247 Dihedral : 14.998 174.004 1066 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.83 % Allowed : 13.37 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.29), residues: 879 helix: 0.70 (0.26), residues: 446 sheet: -1.11 (0.58), residues: 70 loop : -0.89 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 278 TYR 0.021 0.001 TYR B 174 PHE 0.011 0.001 PHE A 290 TRP 0.015 0.001 TRP A 109 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7305) covalent geometry : angle 0.54925 ( 9912) SS BOND : bond 0.00391 ( 2) SS BOND : angle 2.07682 ( 4) hydrogen bonds : bond 0.03982 ( 340) hydrogen bonds : angle 4.31479 ( 978) *********************** 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 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 322 LYS cc_start: 0.7899 (mttm) cc_final: 0.7601 (mttm) REVERT: C 100 ASP cc_start: 0.7316 (t70) cc_final: 0.6792 (t0) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.0669 time to fit residues: 8.4840 Evaluate side-chains 89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR 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 234 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 392 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.203869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.164106 restraints weight = 8252.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.164924 restraints weight = 6830.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.167552 restraints weight = 5980.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.169217 restraints weight = 4057.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.169876 restraints weight = 3722.736| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7307 Z= 0.120 Angle : 0.596 15.822 9916 Z= 0.305 Chirality : 0.041 0.225 1116 Planarity : 0.004 0.047 1247 Dihedral : 14.208 172.472 1066 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.23 % Allowed : 15.60 % Favored : 82.18 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.29), residues: 879 helix: 0.75 (0.26), residues: 448 sheet: -1.12 (0.59), residues: 70 loop : -0.88 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 278 TYR 0.025 0.001 TYR B 174 PHE 0.010 0.001 PHE A 290 TRP 0.014 0.002 TRP A 99 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7305) covalent geometry : angle 0.57036 ( 9912) SS BOND : bond 0.00938 ( 2) SS BOND : angle 8.62670 ( 4) hydrogen bonds : bond 0.03587 ( 340) hydrogen bonds : angle 4.20545 ( 978) *********************** 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 103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 208 PHE cc_start: 0.7877 (t80) cc_final: 0.7565 (t80) REVERT: B 50 MET cc_start: 0.7560 (tpp) cc_final: 0.7342 (mmm) REVERT: B 322 LYS cc_start: 0.7865 (mttm) cc_final: 0.7590 (mttm) REVERT: C 100 ASP cc_start: 0.7344 (t70) cc_final: 0.6817 (t0) outliers start: 17 outliers final: 9 residues processed: 97 average time/residue: 0.0665 time to fit residues: 9.5730 Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 191 CYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 73 optimal weight: 0.0370 chunk 43 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.202297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.161730 restraints weight = 8417.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.165674 restraints weight = 6481.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.167149 restraints weight = 5209.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168678 restraints weight = 3434.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.169199 restraints weight = 3181.586| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7307 Z= 0.114 Angle : 0.573 10.959 9916 Z= 0.295 Chirality : 0.041 0.182 1116 Planarity : 0.004 0.046 1247 Dihedral : 13.591 171.642 1066 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.70 % Allowed : 17.96 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.29), residues: 879 helix: 0.84 (0.26), residues: 449 sheet: -1.20 (0.58), residues: 70 loop : -0.82 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 278 TYR 0.026 0.001 TYR B 174 PHE 0.011 0.001 PHE A 61 TRP 0.028 0.002 TRP A 99 HIS 0.003 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7305) covalent geometry : angle 0.55867 ( 9912) SS BOND : bond 0.00468 ( 2) SS BOND : angle 6.42806 ( 4) hydrogen bonds : bond 0.03465 ( 340) hydrogen bonds : angle 4.14348 ( 978) *********************** 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 97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8750 (pm20) cc_final: 0.8545 (tp-100) REVERT: A 208 PHE cc_start: 0.7922 (t80) cc_final: 0.7638 (t80) REVERT: B 73 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: B 98 MET cc_start: 0.5802 (mmp) cc_final: 0.5202 (mmt) REVERT: B 322 LYS cc_start: 0.7868 (mttm) cc_final: 0.7560 (mttm) REVERT: C 100 ASP cc_start: 0.7366 (t70) cc_final: 0.6800 (t0) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.0645 time to fit residues: 8.9780 Evaluate side-chains 89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 190 CYS Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 50.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.200145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160468 restraints weight = 8671.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.160986 restraints weight = 9083.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.163882 restraints weight = 7289.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.165056 restraints weight = 5121.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.165671 restraints weight = 4792.161| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7307 Z= 0.154 Angle : 0.611 10.707 9916 Z= 0.312 Chirality : 0.043 0.163 1116 Planarity : 0.004 0.070 1247 Dihedral : 13.578 174.132 1066 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.10 % Allowed : 18.22 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.29), residues: 879 helix: 0.63 (0.25), residues: 449 sheet: -0.95 (0.56), residues: 80 loop : -0.91 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.026 0.001 TYR B 174 PHE 0.012 0.001 PHE A 290 TRP 0.015 0.002 TRP A 99 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7305) covalent geometry : angle 0.59712 ( 9912) SS BOND : bond 0.00419 ( 2) SS BOND : angle 6.54718 ( 4) hydrogen bonds : bond 0.04043 ( 340) hydrogen bonds : angle 4.31828 ( 978) *********************** 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 94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.4695 (OUTLIER) cc_final: 0.4383 (tt) REVERT: B 73 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: B 98 MET cc_start: 0.6310 (mmp) cc_final: 0.5544 (mmt) REVERT: C 100 ASP cc_start: 0.7417 (t70) cc_final: 0.6894 (t0) outliers start: 16 outliers final: 9 residues processed: 89 average time/residue: 0.0685 time to fit residues: 8.9422 Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 190 CYS Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET 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 280 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.0270 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 overall best weight: 0.2470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.206964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.171851 restraints weight = 8608.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.170868 restraints weight = 10027.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.173476 restraints weight = 8860.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.175888 restraints weight = 5906.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.175847 restraints weight = 5607.310| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7307 Z= 0.102 Angle : 0.532 9.188 9916 Z= 0.275 Chirality : 0.040 0.159 1116 Planarity : 0.004 0.053 1247 Dihedral : 13.289 172.922 1066 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.44 % Allowed : 18.74 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.30), residues: 879 helix: 0.91 (0.26), residues: 448 sheet: -0.93 (0.54), residues: 83 loop : -0.79 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 272 TYR 0.013 0.001 TYR B 139 PHE 0.009 0.001 PHE A 61 TRP 0.016 0.001 TRP A 99 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 7305) covalent geometry : angle 0.51976 ( 9912) SS BOND : bond 0.00288 ( 2) SS BOND : angle 5.62936 ( 4) hydrogen bonds : bond 0.03241 ( 340) hydrogen bonds : angle 4.06127 ( 978) *********************** 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 97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.4734 (OUTLIER) cc_final: 0.4388 (tt) REVERT: B 98 MET cc_start: 0.6223 (mmp) cc_final: 0.5588 (mmt) REVERT: B 137 ILE cc_start: 0.5412 (mt) cc_final: 0.5188 (mt) REVERT: B 223 TYR cc_start: 0.6827 (p90) cc_final: 0.6606 (p90) REVERT: B 322 LYS cc_start: 0.7997 (mttm) cc_final: 0.7727 (mttm) REVERT: C 100 ASP cc_start: 0.7296 (t70) cc_final: 0.6826 (t0) outliers start: 11 outliers final: 9 residues processed: 96 average time/residue: 0.0646 time to fit residues: 9.1528 Evaluate side-chains 89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 190 CYS Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.203106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.166304 restraints weight = 8772.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.167559 restraints weight = 9049.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.169685 restraints weight = 7702.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.170019 restraints weight = 5193.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.170377 restraints weight = 5483.033| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7307 Z= 0.129 Angle : 0.579 9.741 9916 Z= 0.296 Chirality : 0.041 0.218 1116 Planarity : 0.004 0.051 1247 Dihedral : 13.386 173.841 1066 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.97 % Allowed : 19.27 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.30), residues: 879 helix: 0.85 (0.26), residues: 448 sheet: -0.97 (0.55), residues: 83 loop : -0.85 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 153 TYR 0.015 0.001 TYR A 449 PHE 0.012 0.001 PHE A 290 TRP 0.016 0.002 TRP A 99 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7305) covalent geometry : angle 0.57649 ( 9912) SS BOND : bond 0.00924 ( 2) SS BOND : angle 2.78751 ( 4) hydrogen bonds : bond 0.03663 ( 340) hydrogen bonds : angle 4.13109 ( 978) *********************** 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 96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.4646 (OUTLIER) cc_final: 0.4310 (tt) REVERT: B 73 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: B 98 MET cc_start: 0.6319 (mmp) cc_final: 0.5693 (mmt) REVERT: B 137 ILE cc_start: 0.5425 (mt) cc_final: 0.5221 (mt) REVERT: B 322 LYS cc_start: 0.8031 (mttm) cc_final: 0.7726 (mttm) REVERT: C 100 ASP cc_start: 0.7386 (t70) cc_final: 0.6884 (t0) outliers start: 15 outliers final: 12 residues processed: 93 average time/residue: 0.0704 time to fit residues: 9.6384 Evaluate side-chains 94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 376 ASP 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 280 HIS Chi-restraints excluded: chain B residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.202926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.165810 restraints weight = 8507.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.165486 restraints weight = 9834.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.168351 restraints weight = 8112.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.169429 restraints weight = 5510.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.169603 restraints weight = 5586.843| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7307 Z= 0.128 Angle : 0.574 9.583 9916 Z= 0.292 Chirality : 0.041 0.171 1116 Planarity : 0.004 0.046 1247 Dihedral : 13.449 175.054 1066 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.49 % Allowed : 19.40 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.29), residues: 879 helix: 0.76 (0.26), residues: 449 sheet: -0.94 (0.56), residues: 80 loop : -0.81 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 278 TYR 0.014 0.001 TYR B 139 PHE 0.012 0.001 PHE A 290 TRP 0.017 0.002 TRP A 99 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7305) covalent geometry : angle 0.57237 ( 9912) SS BOND : bond 0.00864 ( 2) SS BOND : angle 2.25329 ( 4) hydrogen bonds : bond 0.03685 ( 340) hydrogen bonds : angle 4.12932 ( 978) *********************** 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 99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.211 Fit side-chains REVERT: A 145 LEU cc_start: 0.4569 (OUTLIER) cc_final: 0.4267 (tt) REVERT: B 73 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: B 98 MET cc_start: 0.6296 (mmp) cc_final: 0.5635 (mmt) REVERT: B 276 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7753 (mm) REVERT: B 322 LYS cc_start: 0.8143 (mttm) cc_final: 0.7873 (mttm) REVERT: C 100 ASP cc_start: 0.7339 (t70) cc_final: 0.6829 (t0) outliers start: 19 outliers final: 14 residues processed: 94 average time/residue: 0.0571 time to fit residues: 7.8998 Evaluate side-chains 94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 383 VAL 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 Chi-restraints excluded: chain B residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.0370 chunk 25 optimal weight: 0.2980 chunk 21 optimal weight: 0.0770 chunk 65 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.208719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.170680 restraints weight = 8662.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.173477 restraints weight = 8876.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.175471 restraints weight = 6594.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.175589 restraints weight = 4869.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.176448 restraints weight = 4450.683| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7307 Z= 0.102 Angle : 0.543 8.390 9916 Z= 0.278 Chirality : 0.040 0.155 1116 Planarity : 0.003 0.048 1247 Dihedral : 13.244 173.499 1066 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.97 % Allowed : 20.18 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.30), residues: 879 helix: 0.98 (0.26), residues: 447 sheet: -1.00 (0.55), residues: 83 loop : -0.75 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 278 TYR 0.014 0.001 TYR B 139 PHE 0.008 0.001 PHE A 387 TRP 0.015 0.001 TRP A 99 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7305) covalent geometry : angle 0.54203 ( 9912) SS BOND : bond 0.00767 ( 2) SS BOND : angle 1.99144 ( 4) hydrogen bonds : bond 0.03250 ( 340) hydrogen bonds : angle 3.99474 ( 978) ********************** 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 103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.307 Fit side-chains REVERT: A 96 MET cc_start: 0.6403 (mmt) cc_final: 0.5953 (mtt) REVERT: A 145 LEU cc_start: 0.4505 (OUTLIER) cc_final: 0.4191 (tt) REVERT: B 73 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: B 98 MET cc_start: 0.6208 (mmp) cc_final: 0.5580 (mmt) REVERT: B 137 ILE cc_start: 0.5224 (mt) cc_final: 0.5015 (mt) REVERT: B 276 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7705 (mm) REVERT: B 322 LYS cc_start: 0.8117 (mttm) cc_final: 0.7857 (mttm) REVERT: C 100 ASP cc_start: 0.7290 (t70) cc_final: 0.6787 (t0) outliers start: 15 outliers final: 10 residues processed: 99 average time/residue: 0.0746 time to fit residues: 10.6977 Evaluate side-chains 92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 223 PHE Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 376 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.206352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.168911 restraints weight = 8634.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.167254 restraints weight = 9089.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.169265 restraints weight = 7392.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.169927 restraints weight = 6347.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.170619 restraints weight = 5512.884| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7307 Z= 0.115 Angle : 0.560 8.530 9916 Z= 0.286 Chirality : 0.041 0.149 1116 Planarity : 0.004 0.046 1247 Dihedral : 13.289 173.874 1066 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.10 % Allowed : 20.31 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.29), residues: 879 helix: 0.90 (0.26), residues: 448 sheet: -1.02 (0.55), residues: 83 loop : -0.77 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.014 0.001 TYR B 139 PHE 0.012 0.001 PHE A 290 TRP 0.016 0.002 TRP A 109 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7305) covalent geometry : angle 0.55850 ( 9912) SS BOND : bond 0.00676 ( 2) SS BOND : angle 2.05555 ( 4) hydrogen bonds : bond 0.03524 ( 340) hydrogen bonds : angle 4.05557 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1215.55 seconds wall clock time: 21 minutes 43.55 seconds (1303.55 seconds total)