Starting phenix.real_space_refine on Thu Jul 2 19:41:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rma_54053/07_2026/9rma_54053_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rma_54053/07_2026/9rma_54053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rma_54053/07_2026/9rma_54053_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rma_54053/07_2026/9rma_54053_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rma_54053/07_2026/9rma_54053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rma_54053/07_2026/9rma_54053.map" } resolution = 3.94 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 S 18 5.16 5 C 3056 2.51 5 N 823 2.21 5 O 918 1.98 5 H 4716 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9532 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 3001 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176} Chain: "C" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6500 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' MN': 1} Classifications: {'water': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.25, per 1000 atoms: 0.13 Number of scatterers: 9532 At special positions: 0 Unit cell: (82.56, 68.37, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 18 16.00 O 918 8.00 N 823 7.00 C 3056 6.00 H 4716 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 409 " distance=2.04 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 420 " distance=2.02 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 241 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 224 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 210.3 milliseconds 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 49.3% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 194 through 200 removed outlier: 4.170A pdb=" N LEU A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.563A pdb=" N GLY A 228 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.606A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'C' and resid 80 through 87 removed outlier: 3.741A pdb=" N HIS C 85 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 115 Proline residue: C 103 - end of helix Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.274A pdb=" N PHE C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 143 Processing helix chain 'C' and resid 158 through 172 Processing helix chain 'C' and resid 179 through 194 removed outlier: 3.729A pdb=" N LEU C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.633A pdb=" N LEU C 216 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 238 removed outlier: 3.846A pdb=" N ALA C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 262 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 308 through 326 Processing helix chain 'C' and resid 331 through 343 removed outlier: 3.676A pdb=" N VAL C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 368 removed outlier: 3.811A pdb=" N THR C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 184 removed outlier: 6.713A pdb=" N LEU A 173 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 140 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 235 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR A 267 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 237 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE A 269 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 239 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.951A pdb=" N ARG C 39 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLY C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 14 262 hydrogen bonds defined for protein. 720 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: 1.57 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.00: 4714 1.00 - 1.21: 2 1.21 - 1.42: 2061 1.42 - 1.63: 2821 1.63 - 1.84: 30 Bond restraints: 9628 Sorted by residual: bond pdb=" CE1 TYR C 407 " pdb=" HE1 TYR C 407 " ideal model delta sigma weight residual 0.930 0.785 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" OH TYR C 407 " pdb=" HH TYR C 407 " ideal model delta sigma weight residual 0.840 0.975 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" CE1 TYR C 407 " pdb=" CZ TYR C 407 " ideal model delta sigma weight residual 1.378 1.218 0.160 2.40e-02 1.74e+03 4.44e+01 bond pdb=" CZ TYR C 407 " pdb=" OH TYR C 407 " ideal model delta sigma weight residual 1.376 1.452 -0.076 2.10e-02 2.27e+03 1.30e+01 bond pdb=" CD1 TYR C 407 " pdb=" CE1 TYR C 407 " ideal model delta sigma weight residual 1.382 1.287 0.095 3.00e-02 1.11e+03 9.93e+00 ... (remaining 9623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.77: 17132 4.77 - 9.53: 188 9.53 - 14.30: 37 14.30 - 19.06: 4 19.06 - 23.83: 2 Bond angle restraints: 17363 Sorted by residual: angle pdb=" CE2 TYR C 407 " pdb=" CZ TYR C 407 " pdb=" OH TYR C 407 " ideal model delta sigma weight residual 119.90 143.73 -23.83 3.00e+00 1.11e-01 6.31e+01 angle pdb=" CE1 TYR C 407 " pdb=" CZ TYR C 407 " pdb=" OH TYR C 407 " ideal model delta sigma weight residual 119.90 99.33 20.57 3.00e+00 1.11e-01 4.70e+01 angle pdb=" CB GLN C 267 " pdb=" CG GLN C 267 " pdb=" CD GLN C 267 " ideal model delta sigma weight residual 112.60 122.27 -9.67 1.70e+00 3.46e-01 3.23e+01 angle pdb=" CD GLU C 56 " pdb=" CG GLU C 56 " pdb=" HG2 GLU C 56 " ideal model delta sigma weight residual 108.00 91.49 16.51 3.00e+00 1.11e-01 3.03e+01 angle pdb=" CA GLN C 267 " pdb=" CB GLN C 267 " pdb=" CG GLN C 267 " ideal model delta sigma weight residual 114.10 124.53 -10.43 2.00e+00 2.50e-01 2.72e+01 ... (remaining 17358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3869 16.62 - 33.25: 450 33.25 - 49.87: 164 49.87 - 66.50: 62 66.50 - 83.12: 15 Dihedral angle restraints: 4560 sinusoidal: 2495 harmonic: 2065 Sorted by residual: dihedral pdb=" CA SER C 22 " pdb=" C SER C 22 " pdb=" N CYS C 23 " pdb=" CA CYS C 23 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 409 " pdb=" CB CYS C 409 " ideal model delta sinusoidal sigma weight residual 93.00 44.98 48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA TYR A 176 " pdb=" C TYR A 176 " pdb=" N SER A 177 " pdb=" CA SER A 177 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 4557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 631 0.085 - 0.169: 88 0.169 - 0.254: 6 0.254 - 0.338: 1 0.338 - 0.423: 1 Chirality restraints: 727 Sorted by residual: chirality pdb=" CB VAL C 336 " pdb=" CA VAL C 336 " pdb=" CG1 VAL C 336 " pdb=" CG2 VAL C 336 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CB VAL C 182 " pdb=" CA VAL C 182 " pdb=" CG1 VAL C 182 " pdb=" CG2 VAL C 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE C 52 " pdb=" CA ILE C 52 " pdb=" CG1 ILE C 52 " pdb=" CG2 ILE C 52 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 724 not shown) Planarity restraints: 1445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 407 " 0.026 2.00e-02 2.50e+03 3.46e-02 3.60e+01 pdb=" CG TYR C 407 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 407 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 407 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR C 407 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR C 407 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 407 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR C 407 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 TYR C 407 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR C 407 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR C 407 " -0.063 2.00e-02 2.50e+03 pdb=" HE2 TYR C 407 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 209 " -0.005 2.00e-02 2.50e+03 2.60e-02 1.52e+01 pdb=" CG HIS C 209 " 0.059 2.00e-02 2.50e+03 pdb=" ND1 HIS C 209 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 HIS C 209 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS C 209 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS C 209 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS C 209 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS C 209 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 HIS C 209 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 408 " 0.007 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" CG TYR C 408 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR C 408 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR C 408 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 408 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 408 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 408 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 408 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 TYR C 408 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR C 408 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR C 408 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR C 408 " 0.029 2.00e-02 2.50e+03 ... (remaining 1442 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 3003 2.35 - 2.91: 21088 2.91 - 3.47: 25135 3.47 - 4.04: 33025 4.04 - 4.60: 49644 Nonbonded interactions: 131895 Sorted by model distance: nonbonded pdb=" OH TYR C 407 " pdb=" HE1 TYR C 407 " model vdw 1.787 1.960 nonbonded pdb=" HE1 TYR C 407 " pdb=" HH TYR C 407 " model vdw 1.793 2.100 nonbonded pdb=" HB2 SER C 385 " pdb=" HG SER C 385 " model vdw 1.945 1.816 nonbonded pdb=" HB VAL C 182 " pdb="HG23 VAL C 182 " model vdw 1.999 1.952 nonbonded pdb=" H ASN C 301 " pdb=" H ARG C 302 " model vdw 2.004 2.100 ... (remaining 131890 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: 1.170 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: 0.030 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.470 Find NCS groups from input model: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.160 4917 Z= 0.344 Angle : 1.302 23.826 6650 Z= 0.649 Chirality : 0.059 0.423 727 Planarity : 0.007 0.075 863 Dihedral : 17.324 83.122 1846 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.37 % Allowed : 20.12 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -1.81 (0.30), residues: 601 helix: -0.60 (0.28), residues: 258 sheet: -1.18 (0.51), residues: 92 loop : -1.74 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.003 ARG C 302 TYR 0.050 0.004 TYR C 408 PHE 0.027 0.003 PHE C 258 TRP 0.016 0.003 TRP C 426 HIS 0.042 0.008 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.34 ( 4912) covalent geometry : angle 1.29691 / 0.65 ( 6638) SS BOND : bond 0.00949 / 0.47 ( 3) SS BOND : angle 1.41133 / 0.78 ( 6) hydrogen bonds : bond 0.15822 / 10.32 ( 254) hydrogen bonds : angle 6.18539 / 4.32 ( 720) link_BETA1-4 : bond 0.00287 / 0.15 ( 1) link_BETA1-4 : angle 4.97239 / 2.68 ( 3) link_NAG-ASN : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : angle 3.07961 / 1.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8629 (mm) cc_final: 0.8353 (tp) REVERT: C 212 MET cc_start: 0.8421 (mmt) cc_final: 0.8193 (mmt) REVERT: C 231 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8826 (pp) REVERT: C 396 MET cc_start: 0.8104 (mmp) cc_final: 0.7676 (mmp) REVERT: C 425 TYR cc_start: 0.8710 (m-80) cc_final: 0.8358 (m-10) outliers start: 7 outliers final: 1 residues processed: 77 average time/residue: 0.1364 time to fit residues: 13.5555 Evaluate side-chains 55 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 282 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN C 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.060328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048608 restraints weight = 78643.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.051397 restraints weight = 39438.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.053268 restraints weight = 24319.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.054594 restraints weight = 16881.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.055534 restraints weight = 12661.948| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4917 Z= 0.146 Angle : 0.593 6.302 6650 Z= 0.307 Chirality : 0.039 0.139 727 Planarity : 0.004 0.044 863 Dihedral : 5.351 34.429 703 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.95 % Allowed : 18.75 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -0.32 (0.34), residues: 601 helix: 1.05 (0.32), residues: 258 sheet: -1.16 (0.49), residues: 97 loop : -1.11 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 284 TYR 0.011 0.001 TYR C 422 PHE 0.007 0.001 PHE C 359 TRP 0.007 0.001 TRP C 338 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 4912) covalent geometry : angle 0.58336 / 0.30 ( 6638) SS BOND : bond 0.00258 / 0.13 ( 3) SS BOND : angle 0.84641 / 0.53 ( 6) hydrogen bonds : bond 0.03823 / 2.67 ( 254) hydrogen bonds : angle 4.93237 / 3.43 ( 720) link_BETA1-4 : bond 0.00139 / 0.07 ( 1) link_BETA1-4 : angle 3.38074 / 1.86 ( 3) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 3.78769 / 1.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8748 (mm) cc_final: 0.8333 (tp) REVERT: C 212 MET cc_start: 0.8168 (mmt) cc_final: 0.7895 (mmt) REVERT: C 231 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8484 (pp) REVERT: C 396 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7689 (mmp) REVERT: C 425 TYR cc_start: 0.8462 (m-80) cc_final: 0.8054 (m-10) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.1524 time to fit residues: 11.2848 Evaluate side-chains 53 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 413 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.056174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.044571 restraints weight = 81739.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.047187 restraints weight = 40360.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.048978 restraints weight = 25126.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.050229 restraints weight = 17797.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.051088 restraints weight = 13666.588| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4917 Z= 0.283 Angle : 0.737 9.693 6650 Z= 0.391 Chirality : 0.043 0.216 727 Planarity : 0.005 0.056 863 Dihedral : 6.004 44.458 700 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.12 % Allowed : 17.58 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -0.80 (0.32), residues: 601 helix: 0.64 (0.31), residues: 262 sheet: -1.47 (0.48), residues: 88 loop : -1.38 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 181 TYR 0.013 0.002 TYR C 422 PHE 0.015 0.002 PHE C 258 TRP 0.020 0.002 TRP C 338 HIS 0.006 0.002 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.28 ( 4912) covalent geometry : angle 0.72469 / 0.39 ( 6638) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 0.57831 / 0.32 ( 6) hydrogen bonds : bond 0.04134 / 2.87 ( 254) hydrogen bonds : angle 5.42843 / 3.80 ( 720) link_BETA1-4 : bond 0.01199 / 0.63 ( 1) link_BETA1-4 : angle 3.82474 / 2.13 ( 3) link_NAG-ASN : bond 0.01072 / 0.56 ( 1) link_NAG-ASN : angle 5.08972 / 2.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 147 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.7799 (p) REVERT: C 149 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: C 396 MET cc_start: 0.7922 (mmp) cc_final: 0.7590 (mmp) REVERT: C 425 TYR cc_start: 0.8645 (m-80) cc_final: 0.8185 (m-10) outliers start: 16 outliers final: 9 residues processed: 52 average time/residue: 0.1310 time to fit residues: 8.8428 Evaluate side-chains 49 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 432 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN C 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.056681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.045486 restraints weight = 78061.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.048104 restraints weight = 37773.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.049840 restraints weight = 22994.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.051075 restraints weight = 15988.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.051978 restraints weight = 12074.166| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4917 Z= 0.118 Angle : 0.573 7.182 6650 Z= 0.292 Chirality : 0.039 0.170 727 Planarity : 0.004 0.041 863 Dihedral : 5.336 42.417 700 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.34 % Allowed : 17.97 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -0.27 (0.33), residues: 601 helix: 1.22 (0.31), residues: 261 sheet: -1.22 (0.48), residues: 88 loop : -1.26 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.008 0.001 TYR C 393 PHE 0.012 0.001 PHE A 180 TRP 0.008 0.001 TRP C 338 HIS 0.003 0.001 HIS C 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 4912) covalent geometry : angle 0.56131 / 0.29 ( 6638) SS BOND : bond 0.00174 / 0.09 ( 3) SS BOND : angle 0.63470 / 0.36 ( 6) hydrogen bonds : bond 0.03447 / 2.44 ( 254) hydrogen bonds : angle 4.88359 / 3.39 ( 720) link_BETA1-4 : bond 0.00320 / 0.17 ( 1) link_BETA1-4 : angle 3.86689 / 2.09 ( 3) link_NAG-ASN : bond 0.00147 / 0.08 ( 1) link_NAG-ASN : angle 3.93465 / 1.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 MET cc_start: 0.9204 (mmm) cc_final: 0.9001 (mmm) REVERT: C 224 MET cc_start: 0.9448 (ppp) cc_final: 0.9115 (tmm) REVERT: C 396 MET cc_start: 0.7799 (mmp) cc_final: 0.7480 (mmp) REVERT: C 425 TYR cc_start: 0.8591 (m-80) cc_final: 0.8048 (m-10) outliers start: 12 outliers final: 11 residues processed: 49 average time/residue: 0.1405 time to fit residues: 8.8541 Evaluate side-chains 48 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 432 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.055741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.044631 restraints weight = 78821.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.047172 restraints weight = 37946.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.048868 restraints weight = 23291.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050083 restraints weight = 16317.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.050980 restraints weight = 12467.245| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4917 Z= 0.156 Angle : 0.574 7.474 6650 Z= 0.294 Chirality : 0.039 0.178 727 Planarity : 0.004 0.041 863 Dihedral : 5.175 41.069 700 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.34 % Allowed : 18.95 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -0.02 (0.34), residues: 601 helix: 1.42 (0.32), residues: 261 sheet: -1.05 (0.49), residues: 86 loop : -1.13 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.007 0.001 TYR C 277 PHE 0.012 0.001 PHE C 258 TRP 0.009 0.001 TRP C 338 HIS 0.004 0.001 HIS C 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 4912) covalent geometry : angle 0.56288 / 0.29 ( 6638) SS BOND : bond 0.00160 / 0.08 ( 3) SS BOND : angle 0.72999 / 0.44 ( 6) hydrogen bonds : bond 0.03232 / 2.30 ( 254) hydrogen bonds : angle 4.73572 / 3.28 ( 720) link_BETA1-4 : bond 0.00244 / 0.13 ( 1) link_BETA1-4 : angle 3.76753 / 2.08 ( 3) link_NAG-ASN : bond 0.00211 / 0.11 ( 1) link_NAG-ASN : angle 3.76183 / 1.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 224 MET cc_start: 0.9398 (ppp) cc_final: 0.9097 (tmm) REVERT: C 425 TYR cc_start: 0.8623 (m-80) cc_final: 0.8094 (m-10) outliers start: 12 outliers final: 11 residues processed: 47 average time/residue: 0.1217 time to fit residues: 7.5908 Evaluate side-chains 46 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 413 TRP Chi-restraints excluded: chain C residue 432 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.056477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.045264 restraints weight = 78836.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.047879 restraints weight = 38223.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049581 restraints weight = 23544.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.050798 restraints weight = 16548.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.051602 restraints weight = 12622.541| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4917 Z= 0.108 Angle : 0.537 7.084 6650 Z= 0.273 Chirality : 0.038 0.157 727 Planarity : 0.004 0.041 863 Dihedral : 4.990 39.340 700 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.15 % Allowed : 20.31 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.22 (0.34), residues: 601 helix: 1.69 (0.32), residues: 261 sheet: -0.90 (0.50), residues: 86 loop : -1.12 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 208 TYR 0.007 0.001 TYR C 393 PHE 0.010 0.001 PHE C 258 TRP 0.007 0.001 TRP C 338 HIS 0.003 0.001 HIS C 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 4912) covalent geometry : angle 0.52644 / 0.27 ( 6638) SS BOND : bond 0.00162 / 0.08 ( 3) SS BOND : angle 0.67441 / 0.39 ( 6) hydrogen bonds : bond 0.03174 / 2.25 ( 254) hydrogen bonds : angle 4.59296 / 3.15 ( 720) link_BETA1-4 : bond 0.00095 / 0.05 ( 1) link_BETA1-4 : angle 3.63196 / 1.98 ( 3) link_NAG-ASN : bond 0.00019 / 0.01 ( 1) link_NAG-ASN : angle 3.44853 / 1.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 224 MET cc_start: 0.9344 (ppp) cc_final: 0.9049 (tmm) REVERT: C 425 TYR cc_start: 0.8556 (m-80) cc_final: 0.8027 (m-10) outliers start: 11 outliers final: 11 residues processed: 45 average time/residue: 0.1398 time to fit residues: 8.1213 Evaluate side-chains 46 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 413 TRP Chi-restraints excluded: chain C residue 432 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.055114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043881 restraints weight = 79216.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.046380 restraints weight = 38600.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.048082 restraints weight = 23896.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049332 restraints weight = 16840.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050159 restraints weight = 12834.818| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4917 Z= 0.173 Angle : 0.572 7.876 6650 Z= 0.296 Chirality : 0.039 0.169 727 Planarity : 0.004 0.040 863 Dihedral : 5.108 39.940 700 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.73 % Allowed : 20.90 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.08 (0.34), residues: 601 helix: 1.53 (0.32), residues: 262 sheet: -0.95 (0.50), residues: 86 loop : -1.15 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 208 TYR 0.008 0.001 TYR C 277 PHE 0.013 0.001 PHE C 258 TRP 0.008 0.001 TRP C 338 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 4912) covalent geometry : angle 0.56156 / 0.29 ( 6638) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 0.74477 / 0.45 ( 6) hydrogen bonds : bond 0.03174 / 2.25 ( 254) hydrogen bonds : angle 4.72045 / 3.26 ( 720) link_BETA1-4 : bond 0.00307 / 0.16 ( 1) link_BETA1-4 : angle 3.58940 / 2.00 ( 3) link_NAG-ASN : bond 0.00394 / 0.21 ( 1) link_NAG-ASN : angle 3.82976 / 1.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 224 MET cc_start: 0.9365 (ppp) cc_final: 0.8961 (tmm) outliers start: 14 outliers final: 11 residues processed: 43 average time/residue: 0.1241 time to fit residues: 7.2531 Evaluate side-chains 42 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 432 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 281 GLN ** 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 = 0.3421 r_free = 0.3421 target = 0.055803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.044334 restraints weight = 78521.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.046896 restraints weight = 38181.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048643 restraints weight = 23596.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.049921 restraints weight = 16624.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.050808 restraints weight = 12682.306| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4917 Z= 0.108 Angle : 0.554 7.248 6650 Z= 0.280 Chirality : 0.039 0.157 727 Planarity : 0.004 0.041 863 Dihedral : 4.873 37.981 700 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.95 % Allowed : 21.48 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.35 (0.34), residues: 601 helix: 1.81 (0.32), residues: 262 sheet: -0.74 (0.51), residues: 86 loop : -1.09 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.007 0.001 TYR C 393 PHE 0.013 0.001 PHE C 258 TRP 0.008 0.001 TRP C 338 HIS 0.003 0.001 HIS C 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 4912) covalent geometry : angle 0.54463 / 0.28 ( 6638) SS BOND : bond 0.00167 / 0.08 ( 3) SS BOND : angle 0.68425 / 0.40 ( 6) hydrogen bonds : bond 0.03098 / 2.20 ( 254) hydrogen bonds : angle 4.54094 / 3.11 ( 720) link_BETA1-4 : bond 0.00101 / 0.05 ( 1) link_BETA1-4 : angle 3.47956 / 1.89 ( 3) link_NAG-ASN : bond 0.00047 / 0.02 ( 1) link_NAG-ASN : angle 3.34532 / 1.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: C 224 MET cc_start: 0.9335 (ppp) cc_final: 0.8898 (tmm) REVERT: C 407 TYR cc_start: 0.7564 (m-10) cc_final: 0.7219 (m-10) outliers start: 10 outliers final: 9 residues processed: 38 average time/residue: 0.1135 time to fit residues: 5.9093 Evaluate side-chains 38 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 413 TRP Chi-restraints excluded: chain C residue 432 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.0020 chunk 55 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 281 GLN ** 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 = 0.3430 r_free = 0.3430 target = 0.056137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.044978 restraints weight = 76977.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.047481 restraints weight = 37086.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049225 restraints weight = 22712.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.050484 restraints weight = 15880.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.051379 restraints weight = 11972.385| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4917 Z= 0.094 Angle : 0.541 8.474 6650 Z= 0.270 Chirality : 0.038 0.157 727 Planarity : 0.003 0.041 863 Dihedral : 4.656 35.196 700 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.15 % Allowed : 20.90 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.57 (0.34), residues: 601 helix: 1.99 (0.32), residues: 262 sheet: -0.51 (0.53), residues: 86 loop : -1.04 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 337 TYR 0.006 0.001 TYR C 393 PHE 0.012 0.001 PHE C 258 TRP 0.007 0.001 TRP C 338 HIS 0.003 0.001 HIS C 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 4912) covalent geometry : angle 0.53185 / 0.27 ( 6638) SS BOND : bond 0.00181 / 0.09 ( 3) SS BOND : angle 0.75112 / 0.44 ( 6) hydrogen bonds : bond 0.03033 / 2.16 ( 254) hydrogen bonds : angle 4.41025 / 3.01 ( 720) link_BETA1-4 : bond 0.00013 / 0.01 ( 1) link_BETA1-4 : angle 3.28627 / 1.79 ( 3) link_NAG-ASN : bond 0.00170 / 0.09 ( 1) link_NAG-ASN : angle 3.19616 / 1.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: C 224 MET cc_start: 0.9258 (ppp) cc_final: 0.8919 (tmm) REVERT: C 425 TYR cc_start: 0.8620 (m-80) cc_final: 0.8094 (m-10) outliers start: 11 outliers final: 9 residues processed: 40 average time/residue: 0.1112 time to fit residues: 6.2174 Evaluate side-chains 39 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 413 TRP Chi-restraints excluded: chain C residue 432 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 281 GLN ** 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 = 0.3407 r_free = 0.3407 target = 0.055228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.044131 restraints weight = 77823.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.046588 restraints weight = 38106.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.048249 restraints weight = 23755.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.049452 restraints weight = 16839.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.050330 restraints weight = 12893.656| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4917 Z= 0.132 Angle : 0.561 8.609 6650 Z= 0.283 Chirality : 0.038 0.155 727 Planarity : 0.004 0.040 863 Dihedral : 4.718 35.728 700 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.76 % Allowed : 21.68 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.48 (0.34), residues: 601 helix: 1.90 (0.32), residues: 262 sheet: -0.55 (0.52), residues: 86 loop : -1.07 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.009 0.001 TYR C 407 PHE 0.012 0.001 PHE C 258 TRP 0.007 0.001 TRP C 338 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 4912) covalent geometry : angle 0.55239 / 0.28 ( 6638) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 0.68605 / 0.40 ( 6) hydrogen bonds : bond 0.03020 / 2.15 ( 254) hydrogen bonds : angle 4.51463 / 3.09 ( 720) link_BETA1-4 : bond 0.00308 / 0.16 ( 1) link_BETA1-4 : angle 3.21907 / 1.78 ( 3) link_NAG-ASN : bond 0.00160 / 0.08 ( 1) link_NAG-ASN : angle 3.49667 / 1.75 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: C 224 MET cc_start: 0.9241 (ppp) cc_final: 0.8881 (tmm) REVERT: C 407 TYR cc_start: 0.7463 (m-10) cc_final: 0.7063 (m-10) REVERT: C 425 TYR cc_start: 0.8632 (m-80) cc_final: 0.8137 (m-10) outliers start: 9 outliers final: 8 residues processed: 38 average time/residue: 0.1484 time to fit residues: 7.6337 Evaluate side-chains 38 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 372 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 281 GLN ** 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 = 0.3407 r_free = 0.3407 target = 0.055298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.044045 restraints weight = 78254.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.046552 restraints weight = 37264.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.048306 restraints weight = 22751.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.049524 restraints weight = 15843.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.050450 restraints weight = 12072.199| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4917 Z= 0.118 Angle : 0.548 8.378 6650 Z= 0.275 Chirality : 0.038 0.151 727 Planarity : 0.004 0.040 863 Dihedral : 4.634 35.641 700 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.56 % Allowed : 21.88 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.52 (0.34), residues: 601 helix: 1.94 (0.32), residues: 262 sheet: -0.53 (0.52), residues: 86 loop : -1.06 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.008 0.001 TYR C 393 PHE 0.011 0.001 PHE C 258 TRP 0.007 0.001 TRP C 338 HIS 0.002 0.001 HIS C 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 4912) covalent geometry : angle 0.53925 / 0.27 ( 6638) SS BOND : bond 0.00177 / 0.09 ( 3) SS BOND : angle 0.75627 / 0.44 ( 6) hydrogen bonds : bond 0.02960 / 2.10 ( 254) hydrogen bonds : angle 4.46312 / 3.04 ( 720) link_BETA1-4 : bond 0.00180 / 0.09 ( 1) link_BETA1-4 : angle 3.18862 / 1.74 ( 3) link_NAG-ASN : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : angle 3.28515 / 1.64 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1541.47 seconds wall clock time: 26 minutes 55.44 seconds (1615.44 seconds total)